A method of manufacturing a liquid discharge head substrate, includes forming an etching mask layer having an opening in a shape corresponding to a plurality of second portions on a second plane of the substrate, forming a recess to be a first portion by etching the substrate through the opening of the etching mask layer from a second plane side of the substrate, and forming the plurality of second portions by etching a portion from a bottom of a first portion to a first plane using the etching mask layer as a mask from the second plane side of the substrate to form a liquid supply port passing through the substrate.