A substrate processing method includes a fluorine-based gas supply step of supplying a fluorine-based gas into a processing chamber where a substrate having a silicon-based film is accommodated, a purge gas supply step of supplying a purge gas for discharging the supplied fluorine-based gas into the processing chamber. The substrate processing method further includes a nitrogen-based gas supply step of supplying a nitrogen-based gas into the processing chamber from which the fluorine-based gas has been discharged. In the substrate processing method, at least in the fluorine-based gas supply step and the purge gas supply step, a temperature of the substrate is maintained at 60° C. or less.