A method of manufacturing a semiconductor device includes carrying a substrate into a process container, forming a thin film on the substrate by supplying a source gas into the process container with the substrate accommodated therein, performing a first modification treatment to a byproduct adhered to an inside of the process container by supplying an oxygen-containing gas and a hydrogen-containing gas into the heated process container under a pressure less than an atmospheric pressure, while accommodating the thin film-formed substrate in the process container, carrying the thin film-formed substrate out of the process container, and performing a second modification treatment to the byproduct adhered to the inside of the process container after the first modification treatment by supplying an oxygen-containing gas and a hydrogen-containing gas into the heated process container under the pressure less than the atmospheric pressure, while not accommodating the substrate in the process container.