A method of fabricating a semiconductor device includes: providing a semiconductor substrate including a hard mask layer; performing, using the hard mask layer, etching to the semiconductor substrate to form a fin-type structure and a groove; forming an isolation material layer in the regions between adjacent fins of the fin-type structure and in the groove; removing a portion of the isolation material layer that is located above the hard mask layer to form a shallow trench isolation; and forming a second mask layer over the hard mask layer, the second mask layer having an opening above the shallow trench isolation; performing ion implantation to the shallow trench isolation through the opening; removing the second mask layer and the hard mask layer; and removing a portion of the isolation material layer located in the regions between adjacent fins of the fin-type structure and a portion of the shallow trench isolation.