A manufacturing method of an integrated circuit includes following steps. A dummy gate with a first mask structure formed thereon and a semiconductor gate with a second mask structure formed thereon are formed on a substrate. A top surface of the semiconductor gate is lower than a top surface of the dummy gate. A first removing process is performed to remove the first mask structure and a part of the second mask structure. A dielectric layer is formed covering the dummy gate, the semiconductor gate, and the second mask structure. A second removing process is performed to remove the dielectric layer above the dummy gate. The dummy gate is removed for forming a trench. A metal gate structure is formed in the trench. The semiconductor gate is covered by the second mask structure during the second removing process and the step of removing the dummy gate.