A manufacturing method of a metal gate structure includes the following steps. First, a substrate covered by an interlayer dielectric is provided. A gate trench is formed in the interlayer dielectric, wherein a gate dielectric layer is formed in the gate trench. A silicon-containing work function layer is formed on the gate dielectric layer in the gate trench. The silicon-containing work function layer includes a vertical portion and a horizontal portion. Finally, the gate trench is filled up with a conductive metal layer.