A method for processing a silicon substrate includes providing a combination of a first silicon substrate, a second silicon substrate, and an intermediate layer including a plurality of recessed portions, which is provided between the first silicon substrate and the second silicon substrate, forming a first through hole that goes through the first silicon substrate by executing etching of the first silicon substrate on a surface of the first silicon substrate opposite to a bonding surface with the intermediate layer by using a first mask, and exposing a portion of the intermediate layer corresponding to the plurality of recessed portions of the intermediate layer, forming a plurality of openings on the intermediate layer by removing a portion constituting a bottom of the plurality of recessed portions, and forming a second through hole that goes through the second silicon substrate by executing second etching of the second silicon substrate by using the intermediate layer on which the plurality of openings are formed as a mask.