diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index 32e51db1ca..522b3e550a 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -356,6 +356,7 @@ if (onnxruntime_BUILD_WEBASSEMBLY)
     # (2) "-flto=thin" does not work correctly for wasm-ld.
     #     we don't set onnxruntime_ENABLE_LTO because it appends flag "-flto=thin"
     #     instead, we manually set CMAKE_CXX_FLAGS "-flto"
+    string(APPEND CMAKE_C_FLAGS " -flto")
     string(APPEND CMAKE_CXX_FLAGS " -flto")
   endif()
 
@@ -368,9 +369,22 @@ if (onnxruntime_BUILD_WEBASSEMBLY)
     set(CMAKE_CXX_FLAGS_DEBUG "-g0")
   endif()
 
+  if (onnxruntime_ENABLE_WEBASSEMBLY_SIMD)
+    string(APPEND CMAKE_C_FLAGS " -msimd128")
+    string(APPEND CMAKE_CXX_FLAGS " -msimd128")
+  endif()
+
+  if (onnxruntime_ENABLE_WEBASSEMBLY_EXCEPTION_CATCHING)
+    string(APPEND CMAKE_C_FLAGS " -s DISABLE_EXCEPTION_CATCHING=0")
+    string(APPEND CMAKE_CXX_FLAGS " -s DISABLE_EXCEPTION_CATCHING=0")
+  endif()
+
   # Build WebAssembly with multi-threads support.
   if (onnxruntime_ENABLE_WEBASSEMBLY_THREADS)
+    string(APPEND CMAKE_C_FLAGS " -pthread")
     string(APPEND CMAKE_CXX_FLAGS " -pthread")
+    string(APPEND CMAKE_C_FLAGS " -s USE_PTHREADS=1 -Wno-pthreads-mem-growth")
+    string(APPEND CMAKE_CXX_FLAGS " -s USE_PTHREADS=1 -Wno-pthreads-mem-growth")
   endif()
 endif()
 
@@ -2130,18 +2144,6 @@ if (onnxruntime_BUILD_CSHARP)
 endif()
 
 if (onnxruntime_BUILD_WEBASSEMBLY)
-  if (onnxruntime_ENABLE_WEBASSEMBLY_SIMD)
-    string(APPEND CMAKE_CXX_FLAGS " -msimd128")
-  endif()
-
-  if (onnxruntime_ENABLE_WEBASSEMBLY_EXCEPTION_CATCHING)
-    string(APPEND CMAKE_CXX_FLAGS " -s DISABLE_EXCEPTION_CATCHING=0")
-  endif()
-
-  if (onnxruntime_ENABLE_WEBASSEMBLY_THREADS)
-    string(APPEND CMAKE_CXX_FLAGS " -s USE_PTHREADS=1 -Wno-pthreads-mem-growth")
-  endif()
-
   message(STATUS "WebAssembly Build is enabled")
   include(onnxruntime_webassembly.cmake)
 endif()
diff --git a/cmake/external/xnnpack.cmake b/cmake/external/xnnpack.cmake
index 7f7307b079..4df57b5ed1 100644
--- a/cmake/external/xnnpack.cmake
+++ b/cmake/external/xnnpack.cmake
@@ -59,10 +59,6 @@ if(onnxruntime_BUILD_WEBASSEMBLY)
     set(${target_srcs} ${bazel_srcs} PARENT_SCOPE)
   endfunction()
 
-  if(onnxruntime_ENABLE_WEBASSEMBLY_THREADS)
-    target_compile_options(XNNPACK PRIVATE "-pthread")
-  endif()
-
   GetSrcListFromBazel("PROD_SCALAR_WASM_MICROKERNEL_SRCS" prod_scalar_wasm_srcs)
   GetSrcListFromBazel("ALL_WASM_MICROKERNEL_SRCS" all_wasm_srcs)
   GetSrcListFromBazel("WASM32_ASM_MICROKERNEL_SRCS" wasm32_asm_srcs)
@@ -82,9 +78,6 @@ if(onnxruntime_BUILD_WEBASSEMBLY)
   if(onnxruntime_ENABLE_WEBASSEMBLY_SIMD)
     GetSrcListFromBazel("ALL_WASMSIMD_MICROKERNEL_SRCS" all_wasmsimd_srcs)
     message(DEBUG "all_wasmsimd_srcs: ${all_wasmsimd_srcs}")
-
-    target_compile_options(params_init PRIVATE "-msimd128")
-    target_compile_options(XNNPACK PRIVATE "-msimd128")
     target_sources(XNNPACK PRIVATE ${all_wasmsimd_srcs})
   endif()
 endif()
diff --git a/tools/ci_build/github/azure-pipelines/templates/web-ci.yml b/tools/ci_build/github/azure-pipelines/templates/web-ci.yml
index 6d31ac3e6a..df53f23a26 100644
--- a/tools/ci_build/github/azure-pipelines/templates/web-ci.yml
+++ b/tools/ci_build/github/azure-pipelines/templates/web-ci.yml
@@ -85,7 +85,7 @@ stages:
         ExtraBuildArgs: '$(ExtraBuildArgs)'
         PoolName: ${{ parameters.PoolName }}
         SkipPublish: true
-        TimeoutInMinutes: 150
+        TimeoutInMinutes: 180
 
 - stage: Build_web_Release
   dependsOn: Build_wasm_Release