A semiconductor device includes a semiconductor substrate, an isolation structure, and a spacer. The semiconductor substrate includes at least one fin structure. The isolation structure is partly disposed in the fin structure and partly disposed above the fin structure. The fin structure includes a first fin and a second fin elongated in the same direction. A part of the isolation structure is disposed between the first fin and the second fin in the direction where the first fin and the second fin are elongated. The spacer is disposed on sidewalls of the isolation structure on the fin structure. The isolation structure in the present invention is partly disposed in the fin structure and partly disposed above the fin structure. The negative influence of a gate structure formed on the isolation structure and sinking into the isolation structure on the isolation performance of the isolation structure may be avoided accordingly.