Provided is a method of manufacturing a semiconductor device, which efficiently removes a high permittivity film (high-k film). The method of manufacturing a semiconductor device includes: (a) supplying a processing gas containing an organic compound into a process chamber to form a predetermined film on a substrate; (b) supplying a first cleaning gas into the process chamber with the substrate being unloaded from the process chamber to remove films adhered to an inner wall of a reaction tube defining the process chamber and members disposed in the process chamber; (c) supplying a modifying gas into the process chamber after performing (b) to modify a carbon-containing film remaining in a nozzle of the members configured to supply the processing gas; and (d) supplying a second cleaning gas into the process chamber to remove a film obtained by modifying the carbon-containing film in (c).