A substrate processing method of processing a substrate using a gas supplied to a chamber includes: (a) setting a threshold value of a pressure of the gas, which is a control target in a flow rate controller configured to measure the pressure of the gas supplied to the chamber and control a flow rate of the gas; (b) supplying the gas into the chamber; (c) measuring the pressure of the gas by the flow rate controller; (d) stopping the supply of the gas into of the chamber; (e) calculating a time when the pressure of the gas measured in (c) becomes equal to or higher than the threshold value; and (f) calculating a total flow rate of the gas supplied into the chamber based on the pressure of the gas measured in (c) and the time calculated in (e).