A method for processing a silicon substrate includes preparing a first silicon substrate including an etching mask layer including first and second opening portions; forming a first recess in a portion of the silicon substrate corresponding to a region in the first opening portion; etching the silicon substrate by crystal anisotropic etching through the etching mask layer with an etching apparatus and an etchant, the etching proceeding in the first and second opening portions to form a through hole in a position corresponding to the first opening portion and to form a second recess in a position corresponding to the second opening portion; calculating an etching rate of the silicon substrate in terms of the etchant by using the second recess; and determining, by using the calculated etching rate, an etching condition for etching another silicon substrate with the etching apparatus after the etching of the first silicon substrate.