A method for manufacturing a semiconductor device having a shallow trench isolation structure includes providing a semiconductor substrate having first and second regions, multiple fins disposed on the first and second regions, and a hardmask layer on an upper surface of the fins, forming a first dielectric layer on the semiconductor substrate covering the fins, forming a first mask layer including an opening exposing a portion of the first dielectric layer between the first and second regions, implanting dopant ions into the exposed portion of the first dielectric layer, removing the first mask layer, and performing an etching process on the first dielectric layer to form a first isolation region between the first and second regions and a second isolation region between the fins. The doped portion has a reduced etch rate so that the thickness of the first isolation region is thicker than the second isolation region.