Efficient cleaning is possible although the film qualities and thicknesses of a reaction tube and a gas supply nozzle are different. There is provided a method of manufacturing a semiconductor device. The method includes forming a film on a substrate, performing a first cleaning process to remove a first deposition substance attached to an inner wall of a gas introducing part, and performing a second cleaning process to remove a second deposition substance attached to an inside of a process chamber and having a chemical composition different from that of the first deposition substance. In the first cleaning process, cleaning conditions are set according to the accumulated supply time of a first source gas supplied to the inside of the process chamber through the gas introducing part, and in the second cleaning process, cleaning conditions are set according to the accumulated thickness of a film formed on the substrate.