A method of manufacturing a semiconductor device including a nitride semiconductor layer having high-precision thickness is provided. The method includes steps of: forming a gallium nitride (GaN) layer whose main face is a +c face on a substrate; forming a trench by selectively etching down a partial region in the +c face of the GaN layer; forming a metal layer so as to bury the trench; and separating the substrate and the GaN layer, after that, polishing a −c face of the GaN layer until the metal layer is exposed, and removing a part in a thickness direction of the GaN layer.