A substrate processing method according to the present invention incudes: a preparation step of preparing a substrate in which at least a first surface containing silicon oxide and a second surface containing silicon or a silicon compound other than silicon oxide are exposed; a surface modification step of forming an etching selectivity imparting film on at least a part of the first surface and at least a part of the second surface by a silylation treatment of bringing a silylating agent into contact with the first surface and the second surface; and an etching step of selectively carrying out an etching treatment on the second surface with respect to the first surface using an etching agent after the surface modification step.