diff --git a/.github/workflows/rust.yml b/.github/workflows/rust.yml
index 06c2a50..5e1cefc 100644
--- a/.github/workflows/rust.yml
+++ b/.github/workflows/rust.yml
@@ -45,6 +45,16 @@ jobs:
       run: cd test-workspace && rustup target add riscv64imac-unknown-none-elf && rustup component add clippy
     - name: Run all checks
       run: cd test-workspace && make build test check clippy
+    - name: Generate native simulators for coverage
+      if: matrix.os == 'ubuntu-latest'
+      run: cd test-workspace &&
+        make generate-native-simulator CRATE=c1 TEMPLATE_TYPE=--path TEMPLATE_REPO=..
+    - name: Install llvm-tools for coverage
+      if: matrix.os == 'ubuntu-latest'
+      run: cd test-workspace && make coverage-install
+    - name: Run coverage tests
+      if: matrix.os == 'ubuntu-latest'
+      run: cd test-workspace && make coverage
     - name: Reproducible build runs
       run: cd test-workspace && ./scripts/reproducible_build_docker --update && ./scripts/reproducible_build_docker --no-clean
     - name: Generate standalone contract
diff --git a/README.md b/README.md
index fad96b9..32214e2 100644
--- a/README.md
+++ b/README.md
@@ -255,3 +255,47 @@ make generate-native-simulator CRATE=example_crate
 
 - The `CRATE` parameter must refer to a subproject.
 - Missing subprojects will cause the command to fail.
+
+### Code Coverage
+
+The templates include built-in support for code coverage reporting using LLVM's coverage tools.
+
+**Requirements:**
+- Only contracts created with the `contract` template support coverage (pure Rust contracts with `native-simulator` feature)
+- Other templates (`atomics-contract`, `stack-reorder-contract`, `contract-without-simulator`, `standalone-contract`) do not support coverage
+- Native simulators must be generated for each contract you want coverage for
+- Only works on x86_64 Linux (not ARM)
+
+**Setup:**
+
+1. Install llvm-tools:
+```bash
+make coverage-install
+```
+
+2. Generate native simulators for your contracts:
+```bash
+make generate-native-simulator CRATE=<contract_name>
+```
+
+**Generate Reports:**
+```bash
+make coverage        # Text report to console
+make coverage-html   # HTML report in target/coverage/html/
+make coverage-lcov   # LCOV format for CI integration
+```
+
+**Example:**
+```bash
+# Create a contract using the default 'contract' template
+make generate CRATE=my-contract
+
+# Generate native simulator for it
+make generate-native-simulator CRATE=my-contract
+
+# Install tools and run coverage
+make coverage-install
+make coverage
+```
+
+Coverage works by running tests with the `native-simulator` feature, which executes contract code natively on x86_64 instead of in CKB-VM. This allows LLVM's coverage instrumentation to track which lines of code are executed.
diff --git a/atomics-contract/.cargo-generate/tests.rs b/atomics-contract/.cargo-generate/tests.rs
index b763d6b..f19ca2f 100644
--- a/atomics-contract/.cargo-generate/tests.rs
+++ b/atomics-contract/.cargo-generate/tests.rs
@@ -4,8 +4,7 @@
 fn test_{{crate_name}}() {
     // deploy contract
     let mut context = Context::default();
-    let contract_bin: Bytes = Loader::default().load_binary("{{project-name}}");
-    let out_point = context.deploy_cell(contract_bin);
+    let out_point = context.deploy_cell_by_name("{{project-name}}");
 
     // prepare scripts
     let lock_script = context
diff --git a/contract-without-simulator/.cargo-generate/tests.rs b/contract-without-simulator/.cargo-generate/tests.rs
index b763d6b..f19ca2f 100644
--- a/contract-without-simulator/.cargo-generate/tests.rs
+++ b/contract-without-simulator/.cargo-generate/tests.rs
@@ -4,8 +4,7 @@
 fn test_{{crate_name}}() {
     // deploy contract
     let mut context = Context::default();
-    let contract_bin: Bytes = Loader::default().load_binary("{{project-name}}");
-    let out_point = context.deploy_cell(contract_bin);
+    let out_point = context.deploy_cell_by_name("{{project-name}}");
 
     // prepare scripts
     let lock_script = context
diff --git a/contract/.cargo-generate/tests.rs b/contract/.cargo-generate/tests.rs
index b763d6b..f19ca2f 100644
--- a/contract/.cargo-generate/tests.rs
+++ b/contract/.cargo-generate/tests.rs
@@ -4,8 +4,7 @@
 fn test_{{crate_name}}() {
     // deploy contract
     let mut context = Context::default();
-    let contract_bin: Bytes = Loader::default().load_binary("{{project-name}}");
-    let out_point = context.deploy_cell(contract_bin);
+    let out_point = context.deploy_cell_by_name("{{project-name}}");
 
     // prepare scripts
     let lock_script = context
diff --git a/native-simulator/Cargo.toml b/native-simulator/Cargo.toml
index 203488c..847813c 100644
--- a/native-simulator/Cargo.toml
+++ b/native-simulator/Cargo.toml
@@ -3,10 +3,13 @@ name = "{{project-name}}"
 version = "0.1.0"
 edition = "2024"
 
-# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
 [dependencies]
 {{project-name | append: "@@SIMULATOR_PLACEHOLDER@@" | remove: "-sim@@SIMULATOR_PLACEHOLDER@@"}} = { path = "../../contracts/{{project-name | append: "@@SIMULATOR_PLACEHOLDER@@" | remove: "-sim@@SIMULATOR_PLACEHOLDER@@"}}", features = ["native-simulator"] }
 ckb-std = { version = "1.0", features = ["native-simulator"] }
+ctor = "0.6"
 
 [lib]
 crate-type = ["cdylib"]
+
+[lints.rust]
+unexpected_cfgs = { level = "warn", check-cfg = ['cfg(coverage)'] }
diff --git a/native-simulator/src/lib.rs b/native-simulator/src/lib.rs
index 26128b7..a66475c 100644
--- a/native-simulator/src/lib.rs
+++ b/native-simulator/src/lib.rs
@@ -1 +1,18 @@
 ckb_std::entry_simulator!({{project-name | append: "@@SIMULATOR_PLACEHOLDER@@" | remove: "-sim@@SIMULATOR_PLACEHOLDER@@" | replace: "-", "_"}}::program_entry);
+
+// Flush LLVM coverage data when the shared library is unloaded.
+// This is necessary because coverage data from dynamically loaded libraries
+// is not automatically written when using cargo-llvm-cov.
+#[cfg(coverage)]
+mod coverage_flush {
+    unsafe extern "C" {
+        fn __llvm_profile_write_file() -> i32;
+    }
+
+    #[ctor::dtor]
+    fn flush_coverage() {
+        unsafe {
+            __llvm_profile_write_file();
+        }
+    }
+}
diff --git a/stack-reorder-contract/.cargo-generate/tests.rs b/stack-reorder-contract/.cargo-generate/tests.rs
index b763d6b..f19ca2f 100644
--- a/stack-reorder-contract/.cargo-generate/tests.rs
+++ b/stack-reorder-contract/.cargo-generate/tests.rs
@@ -4,8 +4,7 @@
 fn test_{{crate_name}}() {
     // deploy contract
     let mut context = Context::default();
-    let contract_bin: Bytes = Loader::default().load_binary("{{project-name}}");
-    let out_point = context.deploy_cell(contract_bin);
+    let out_point = context.deploy_cell_by_name("{{project-name}}");
 
     // prepare scripts
     let lock_script = context
diff --git a/workspace/Makefile b/workspace/Makefile
index 36a9c7e..c0dfbe8 100644
--- a/workspace/Makefile
+++ b/workspace/Makefile
@@ -150,4 +150,139 @@ CHECKSUM_FILE := build/checksums-$(MODE).txt
 checksum: build
 	shasum -a 256 build/$(MODE)/* > $(CHECKSUM_FILE)
 
-.PHONY: build test check clippy fmt cargo clean prepare checksum
+# ============================================================================
+# Coverage targets (using native-simulator mode)
+# ============================================================================
+#
+# Coverage works by:
+# 1. Building simulator .so files with LLVM coverage instrumentation
+# 2. Running tests with native-simulator feature (executes contracts natively)
+# 3. Simulator .so files call __llvm_profile_write_file() on unload to flush coverage
+# 4. Using llvm-cov to generate reports from the profraw files
+#
+# Requirements: rustup component add llvm-tools-preview
+#
+# Usage:
+#   make coverage          # Generate text coverage report
+#   make coverage-html     # Generate HTML coverage report
+#   make coverage-lcov     # Generate LCOV format for CI integration
+
+LLVM_TOOLS_DIR := $(shell rustc --print sysroot)/lib/rustlib/$(shell rustc -vV | grep host | cut -d' ' -f2)/bin
+LLVM_PROFDATA := $(LLVM_TOOLS_DIR)/llvm-profdata
+LLVM_COV := $(LLVM_TOOLS_DIR)/llvm-cov
+COVERAGE_DIR := target/coverage
+PROFRAW_PATTERN := $(COVERAGE_DIR)/profraw
+
+# Dynamically find all simulator .so files
+SIMULATOR_OBJECTS = $(wildcard build/debug/lib*_sim.so)
+SIMULATOR_OBJECT_ARGS = $(foreach obj,$(SIMULATOR_OBJECTS),-object $(obj))
+
+# Build simulators with coverage instrumentation
+build-sim-cov:
+	@echo "Building native simulators with coverage instrumentation..."
+	@# First build the RISC-V contract binaries (these don't need coverage)
+	$(MAKE) build MODE=debug CLEAN_BUILD_DIR_FIRST=true
+	@# Clean simulator artifacts to force rebuild with coverage
+	@rm -f target/debug/deps/lib*_sim*.rlib
+	@rm -f target/debug/lib*_sim.so
+	@# Rebuild simulators with LLVM coverage instrumentation
+	@echo "Rebuilding simulators with LLVM coverage instrumentation..."
+	@for sim in $(wildcard native-simulators/*); do \
+		simname=$$(basename $$sim); \
+		RUSTFLAGS="-C instrument-coverage --cfg=coverage" \
+			cargo build -p $$simname; \
+	done
+	@# Copy the instrumented simulators to build/debug/
+	@echo "Copying instrumented simulators to build/debug/..."
+	@for sim in $(wildcard native-simulators/*); do \
+		simname=$$(basename $$sim); \
+		libname=$$(echo $$simname | sed 's/-/_/g'); \
+		if [ -f "target/debug/lib$${libname}.so" ]; then \
+			cp "target/debug/lib$${libname}.so" build/debug/; \
+		fi; \
+	done
+	@echo "Done! Instrumented simulators are in build/debug/"
+
+# Build simulators for coverage (debug mode for better coverage data)
+build-sim:
+	@echo "Building native simulators..."
+	$(MAKE) build MODE=debug CLEAN_BUILD_DIR_FIRST=true
+
+# Internal target: run tests and collect coverage data
+coverage-run-tests:
+	@echo "Running tests with coverage (native-simulator mode)..."
+	@mkdir -p $(COVERAGE_DIR)
+	@rm -f $(PROFRAW_PATTERN)-*.profraw
+	@# Run all tests with native-simulator feature and coverage instrumentation
+	LLVM_PROFILE_FILE="$(CURDIR)/$(PROFRAW_PATTERN)-%p-%8m.profraw" \
+		RUSTFLAGS="-C instrument-coverage" \
+		MODE=debug cargo test --features native-simulator --package tests \
+		-- --test-threads=1 2>&1 || true
+	@echo "Merging coverage data..."
+	@if ls $(PROFRAW_PATTERN)-*.profraw 1> /dev/null 2>&1; then \
+		$(LLVM_PROFDATA) merge -sparse $(PROFRAW_PATTERN)-*.profraw -o $(COVERAGE_DIR)/coverage.profdata; \
+		rm -f $(PROFRAW_PATTERN)-*.profraw; \
+	else \
+		echo "Warning: No profraw files found. Tests may have failed or no coverage data was generated."; \
+	fi
+	@# Clean up stray default_*.profraw files created by child processes
+	@rm -f $(CURDIR)/default_*.profraw
+
+# Run tests with coverage and generate text report
+coverage: build-sim-cov coverage-run-tests
+	@echo ""
+	@echo "=== Coverage Report ==="
+	@if [ -f "$(COVERAGE_DIR)/coverage.profdata" ]; then \
+		$(LLVM_COV) report \
+			$(SIMULATOR_OBJECT_ARGS) \
+			-instr-profile=$(COVERAGE_DIR)/coverage.profdata \
+			--ignore-filename-regex='\.cargo|rustc|rustlib'; \
+	else \
+		echo "Error: No coverage data found. Run 'make coverage-install' to install llvm-tools."; \
+	fi
+
+# Generate HTML coverage report
+coverage-html: build-sim-cov coverage-run-tests
+	@echo "Generating HTML coverage report..."
+	@mkdir -p $(COVERAGE_DIR)/html
+	@if [ -f "$(COVERAGE_DIR)/coverage.profdata" ]; then \
+		$(LLVM_COV) show \
+			$(SIMULATOR_OBJECT_ARGS) \
+			-instr-profile=$(COVERAGE_DIR)/coverage.profdata \
+			--ignore-filename-regex='\.cargo|rustc|rustlib' \
+			--format=html --output-dir=$(COVERAGE_DIR)/html \
+			--show-line-counts-or-regions --show-instantiations; \
+		echo "Coverage report generated at: $(COVERAGE_DIR)/html/index.html"; \
+	else \
+		echo "Error: No coverage data found."; \
+	fi
+
+# Generate LCOV format for CI integration
+coverage-lcov: build-sim-cov coverage-run-tests
+	@echo "Generating LCOV coverage report..."
+	@if [ -f "$(COVERAGE_DIR)/coverage.profdata" ]; then \
+		$(LLVM_COV) export \
+			$(SIMULATOR_OBJECT_ARGS) \
+			-instr-profile=$(COVERAGE_DIR)/coverage.profdata \
+			--ignore-filename-regex='\.cargo|rustc|rustlib' \
+			--format=lcov > $(COVERAGE_DIR)/lcov.info; \
+		echo "LCOV report generated at: $(COVERAGE_DIR)/lcov.info"; \
+	else \
+		echo "Error: No coverage data found."; \
+	fi
+
+# Install llvm-tools if not present
+coverage-install:
+	@if ! rustup component list --installed | grep -q llvm-tools; then \
+		echo "Installing llvm-tools-preview..."; \
+		rustup component add llvm-tools-preview; \
+	else \
+		echo "llvm-tools-preview is already installed"; \
+	fi
+
+# Clean coverage artifacts
+coverage-clean:
+	rm -rf $(COVERAGE_DIR)
+
+.PHONY: build test check clippy fmt cargo clean prepare checksum \
+        build-sim build-sim-cov coverage-run-tests coverage coverage-html coverage-lcov coverage-install coverage-clean
diff --git a/workspace/tests/src/tests.rs b/workspace/tests/src/tests.rs
index e6353c3..32e0c04 100644
--- a/workspace/tests/src/tests.rs
+++ b/workspace/tests/src/tests.rs
@@ -1,10 +1,4 @@
-use crate::Loader;
-use ckb_testtool::ckb_types::{
-    bytes::Bytes,
-    core::TransactionBuilder,
-    packed::*,
-    prelude::*,
-};
+use ckb_testtool::ckb_types::{bytes::Bytes, core::TransactionBuilder, packed::*, prelude::*};
 use ckb_testtool::context::Context;
 
 // Include your tests here