diff --git a/onnxruntime/core/providers/webgpu/webgpu_execution_provider.cc b/onnxruntime/core/providers/webgpu/webgpu_execution_provider.cc
index 3df194217933e..15b2d2ece137e 100644
--- a/onnxruntime/core/providers/webgpu/webgpu_execution_provider.cc
+++ b/onnxruntime/core/providers/webgpu/webgpu_execution_provider.cc
@@ -935,13 +935,14 @@ std::unique_ptr<onnxruntime::IExternalDataLoader> WebGpuExecutionProvider::GetEx
 std::optional<bool> WebGpuExecutionProvider::ShouldConvertDataLayoutForOp(std::string_view node_domain,
                                                                           std::string_view node_op_type,
                                                                           DataLayout target_data_layout) const {
-  if (target_data_layout != DataLayout::NHWC) {
-    return std::nullopt;
-  }
-
   // NHWC for Resize operator is not implemented on kWebGpuExecutionProvider
   if (node_domain == kOnnxDomain && node_op_type == "Resize") {
-    return false;
+    return target_data_layout != DataLayout::NHWC;
+  }
+
+  // WebGPU perfer NCHW for InstanceNormalization due to a better performance
+  if (node_domain == kOnnxDomain && node_op_type == "InstanceNormalization") {
+    return target_data_layout != DataLayout::NHWC;
   }
 
   return std::nullopt;