diff --git a/js/web/lib/wasm/jsep/webgpu/ops/instance-norm.ts b/js/web/lib/wasm/jsep/webgpu/ops/instance-norm.ts
index 859bd850862aa..a357d29667319 100644
--- a/js/web/lib/wasm/jsep/webgpu/ops/instance-norm.ts
+++ b/js/web/lib/wasm/jsep/webgpu/ops/instance-norm.ts
@@ -36,7 +36,10 @@ const computeChannelScaleShift = (
   const f32Type = components === 1 ? 'f32' : `vec${components}f`;
   const wgType = components === 1 ? 'vec2f' : `mat2x${components}f`;
   const unitsOfWork = n * c;
-
+  let workgroupSize = 64;
+  if (unitsOfWork === 1) {
+    workgroupSize = 256;
+  }
   const inputShape = [n, c, h / components];
   const outputShape = [n, c, 2];
   const inputDependencies: ProgramInputTensorInfoDependency[] = ['rank', 'type', 'type'];
@@ -49,7 +52,6 @@ const computeChannelScaleShift = (
     const b = inputVariable('bias', bias.dataType, bias.dims);
     const output = outputVariable('output', DataType.float, 3, 2);
     const variables = [x, s, b, output];
-    const workgroupSize = 64;
     return `
   var<workgroup> workgroup_shared : array<${wgType}, ${workgroupSize}>;
   const workgroup_size = ${workgroupSize}u;
@@ -91,7 +93,7 @@ const computeChannelScaleShift = (
     {
       name: 'InstanceNormComputeChannelScaleShift',
       // TODO: use epsilon as uniform. Currently epsilon as uniform fails test_instancenorm_epsilon.
-      shaderCache: { hint: `${components};${epsilon}`, inputDependencies },
+      shaderCache: { hint: `${components};${epsilon};${workgroupSize}`, inputDependencies },
       getRunData: () => ({
         outputs: [{ dims: outputShape, dataType: DataType.float }],
         dispatchGroup: { x: unitsOfWork },
@@ -187,14 +189,21 @@ const createInstanceNormNHWCProgramInfo = (
   const inputDependencies: ProgramInputTensorInfoDependency[] = ['type', 'type'];
 
   // 1. transpose x from NHWC to NCHW
+  let needTranspose = false;
   const transposedXPerm = [0, xShape.length - 1];
   for (let i = 0; i < xShape.length - 2; i++) {
+    needTranspose = needTranspose || xShape[i + 1] !== 1;
     transposedXPerm.push(i + 1);
   }
-  const transposedX = context.compute(createTransposeProgramInfo(context.inputs[0], transposedXPerm), {
-    inputs: [context.inputs[0]],
-    outputs: [-1],
-  })[0];
+
+  needTranspose = needTranspose && xShape[xShape.length - 1] !== 1;
+
+  const transposedX = needTranspose
+    ? context.compute(createTransposeProgramInfo(context.inputs[0], transposedXPerm), {
+        inputs: [context.inputs[0]],
+        outputs: [-1],
+      })[0]
+    : context.inputs[0].reshape(Array.from({ length: xShape.length }, (_, i) => xShape[transposedXPerm[i]]));
   // 2. compute channel scale and channel shift.
   const channelScaleShift = computeChannelScaleShift(
     context,