A method for fabricating semiconductor device includes the steps of first forming a first trench and a second trench in a substrate and then forming a shallow trench isolation (STI) in the first trench, in which the STI comprises a top portion and a bottom portion and a top surface of the top portion is even with or higher than a bottom surface of the second trench. Next, a conductive layer is formed in the first trench and the second trench to form a first gate structure and a second gate structure.