A substrate processing apparatus cleaning method that includes: containing a cleaning gas in a reaction tube without generating a gas flow of the cleaning gas in the reaction tube by supplying the cleaning gas into the reaction tube and by completely stopping exhaustion of the cleaning gas from the reaction tube or by exhausting the cleaning gas at an exhausting rate which substantially does not affect uniform diffusion of the cleaning gas in the reaction tube from at a point of time of a period from a predetermined point of time before the cleaning gas is supplied into the reaction tube to a point of time when several seconds are elapsed after starting of supply of the cleaning gas into the reaction tube; and thereafter exhausting the cleaning gas from the reaction tube.