There is provided a method of manufacturing a nitride semiconductor device. The method of manufacturing the nitride semiconductor device comprises: a first film forming process that forms a first film on a nitride semiconductor layer; an ion implantation process that implants a P-type impurity into the nitride semiconductor layer through the first film by ion implantation; a second film forming process that forms a second film on the first film, after the ion implantation process; and a heat treatment process that processes the nitride semiconductor layer by heat treatment after the second film forming process. This suppresses the surface of the nitride semiconductor layer from being roughened.