A manufacturing method of a semiconductor device includes the following steps. A semiconductor substrate including at least one fin structure is provided. A gate material layer is formed on the semiconductor substrate, and the fin structure is covered by the gate material layer. A trench is formed partly in the gate material layer and partly in the fin structure. An isolation structure is formed partly in the trench and partly outside the trench. At least one gate structure is formed straddling the fin structure by patterning the gate material layer after the step of forming the isolation structure. A top surface of the isolation structure is higher than a top surface of the gate structure in a vertical direction for enhancing the isolation performance of the isolation structure. A sidewall spacer is formed on sidewalls of the isolation structure, and there is no gate structure formed on the isolation structure.