A substrate processing method that can selectively remove deposit produced through dry etching of silicon. A substrate has a silicon base material and a hard mask that is made of a silicon nitride film and/or a silicon oxide film and formed on the silicon base material, the hard mask having an opening to which at least part of the silicon base material is exposed. A trench corresponding to the opening is formed in the silicon base material through dry etching using plasma produced from halogenated gas. After the dry etching, the substrate is heated to a temperature of not less than 200° C., and then hydrogen fluoride gas and helium gas are supplied toward the substrate.