A substrate processing method for reducing a surface roughness of a semiconductor wafer by processing a film structure having at least two types of films beforehand disposed on the substrate, including steps of repeating an adsorption step of supplying activated particles into the processing chamber and allowing the particles to be adsorbed to a surface of a desirable film to be etched in the at least two types of films to allow the particles to combine with a material of the desirable film to form a reaction layer, a removal step of using plasma generated by supplying oxygen into the processing chamber to remove a deposit containing particles adhering to a surface of an undesirable film to be etched in the films, and a desorption step of desorbing and removing the reaction layer on the desirable film to be etched by heating the sample.