A method for fabricating semiconductor device is disclosed. The method includes the steps of: providing a substrate having a first region and a second region; forming a plurality of fin-shaped structures and a first shallow trench isolation (STI) around the fin-shaped structures on the first region and the second region; forming a patterned hard mask on the second region; removing the fin-shaped structures and the first STI from the first region; forming a second STI on the first region; removing the patterned hard mask; and forming a gate structure on the second STI.