A method for fabricating semiconductor device is disclosed. The method includes the steps of: providing a substrate having at least one fin-shaped structure thereon, wherein the fin-shaped structure comprises a top portion and a bottom portion; removing part of the bottom portion of the fin-shaped structure; forming an epitaxial layer on the substrate to surround the bottom portion of the fin-shaped structure; transforming the bottom portion of the fin-shaped structure into the epitaxial layer; and removing part of the epitaxial layer.