A method of manufacturing a semiconductor device including a semiconductor layer and a dielectric layer deposited on the semiconductor layer, including: forming the semiconductor layer; performing a surface treatment for removing a residual carbon compound, on a surface of the semiconductor layer formed; forming a dielectric film under a depositing condition corresponding to a surface state after the surface treatment, on at least a part of the surface of the semiconductor layer on which the surface treatment has been performed; and changing a crystalline state of at least a partial region of the semiconductor layer by performing a heat treatment on the semiconductor layer on which the dielectric film has been formed.