A substrate processing method includes: forming a coating film so as to cover a front surface of the substrate, the substrate having a recess formed in the front surface and in which an organic film is formed; heating the substrate to turn the organic film into a gas, removing the gas from an interior of the recess by causing the gas to pass through the coating film, and forming in the substrate a sealed space surrounded by the recess and the coating film; supplying a processing gas into the sealed space; and irradiating the substrate with a light to activate the processing gas in the sealed space, causing a reaction product gas to pass through the coating film, and removing the reaction product gas, wherein the reaction product gas is generated by a reaction between a residue of the organic film and the activated processing gas in the sealed space.