A method of manufacturing a semiconductor device includes supplying a process gas into a process vessel accommodating a substrate to form a thin film on the substrate and supplying a cleaning gas into the process vessel to clean an inside of the process vessel, after the supplying the process gas to form the thin film is performed a predetermined number of times. When cleaning the inside of the process vessel, a fluorine-containing gas, an oxygen-containing gas and a hydrogen-containing gas are supplied as the cleaning gas into the process vessel heated and kept at a pressure less than an atmospheric pressure to remove a deposit including the thin film adhering to the inside of the process vessel through a thermochemical reaction.