A substrate processing apparatus including: a first valve provided between a gas supply source and an air-water separation tank, the first valve opening and closing a flow path of a gas supplied from the gas supply source; a second valve that opens and closes a flow path of liquid discharged from a discharge port of the air-water separation tank; and a control unit that controls the first valve and the second valve. The discharge port of the air-water separation tank communicates with a discharge port of a cleaning chamber that cleans the substrate, and the control unit controls to close the first valve after preset gas supply time elapses from when the first valve is opened and gas can no longer be discharged from the air-water separation tank and controls to close the second valve after the first valve is closed.