Methods of modifying a self-aligned contact process in a semiconductor fabrication and a semiconductor device are provided. A method includes forming a transistor over a substrate, including depositing a high-k dielectric layer over the substrate; depositing a work function metal layer over the high-k dielectric layer; forming a metal gate over the work function metal layer; forming two spacers sandwiching the work function metal layer and the metal gate; and forming a doped region in the substrate; etching the work function metal layer and the metal gate to leave a metal residue over inner walls of the two spacers exposing the work function metal layer and the metal gate; modifying the metal residue and the exposed work function metal layer and metal gate to form a metal compound; depositing an insulator covering the metal compound; and forming contact pads respectively electrically connected to the metal gate and the doped region.