A method for manufacturing a liquid-ejection head substrate including a silicon substrate having a supply port for supplying liquid is provided. The method includes: forming an etching mask layer on a surface of the silicon substrate, the etching mask layer having an opening in a portion corresponding to the supply port; forming a first recess in the surface of the silicon substrate by anisotropically etching the silicon substrate through the opening in the etching mask layer; forming a second recess that extends toward the other surface of the silicon substrate, in a surface of the first recess in the silicon substrate; and forming the supply port by anisotropically etching the silicon substrate from the surface provided with the second recess.