A method of manufacturing a semiconductor device has: carrying a substrate into a process chamber; depositing a thin film on the substrate by supplying inside the process chamber a first film deposition gas including at least one element among plural elements forming a thin film to be deposited and capable of accumulating a film solely and a second film deposition gas including at least another element among the plural elements and incapable of accumulating a film solely; carrying the substrate on which is deposited the thin film out from inside the process chamber; and removing a first sediment adhering to an interior of the process chamber and a second sediment adhering to an interior of the supply portion and having a chemical composition different from a chemical composition of the first sediment by supplying cleaning gases inside the process chamber and inside a supply portion that supplies the first film deposition gas while changing at least one of a supply flow rate, a concentration, and a type between a cleaning gas to be supplied inside the process chamber and a cleaning gas to be supplied inside the supply portion.