There is provided a cleaning method of a substrate processing apparatus comprising cleaning an inside of an exhaust pipe through which a gas of an inside of a processing container is exhausted. The cleaning the inside of the exhaust pipe includes: removing a deposit on a downstream side of an opening/closing valve in the exhaust pipe by supplying a first exhaust pipe cleaning gas containing fluorine to the downstream side of the opening/closing valve in the exhaust pipe in a state in which the opening/closing valve provided in a middle of the exhaust pipe is closed; and removing a deposit on an upstream side of the opening/closing valve in the exhaust pipe by supplying a second exhaust pipe cleaning gas not containing fluorine as a gas constituent element to the inside of the processing container in a state in which the opening/closing valve is opened.