A method for fabricating semiconductor device is disclosed. First, a substrate is provided, a first fin-shaped structure and a bump are formed on the substrate, and an insulating layer is formed on the bump and around the first fin-shaped structure. Next, a part of the first fin-shaped structure is removed, an epitaxial layer is formed on the first fin-shaped structure, part of the epitaxial layer is removed, and part of the insulating layer is removed to form a shallow trench isolation (STI) and a second fin-shaped structure protruding from the STI. Preferably, the second fin-shaped structure includes a top portion and a bottom portion, in which the bottom portion and the bump are made of same material.