A method of manufacturing a semiconductor device, having the steps of: (a) forming a first gate insulating film having a first thickness in a plurality of regions on a surface of a semiconductor substrate; (b) removing the first gate insulating film in a first region among the plurality of regions and allowing a native oxide film to be formed; (c) heating the semiconductor substrate in a reducing atmosphere and selectively reducing and removing the native oxide film formed in the step (b); and (d) after the step (c), forming a second gate insulating film having a second thickness thinner than the first thickness on the surface of the semiconductor substrate in the first region.