The present disclosure provides a semiconductor structure having a fin structure and a method of manufacturing the semiconductor structure. The semiconductor includes a substrate defined with an active region. A first gate structure is disposed in the active region and includes a dielectric material. A second gate structure is disposed in the active region and includes the dielectric material. A fin structure having a first top surface is arranged to alternate with the first gate structure and the second gate structure. The first gate structure has a second top surface and the second gate structure has a third top surface. The second top surface and the third top surface are lower than the first top surface.