A method of manufacturing a patterned substrate includes: providing an exposure mask that includes: a plurality of inner light-shielding portions arranged in a lattice, a light-transmissive portion integrally connecting regions surrounding the plurality of inner light-shielding portions, and an outer light-shielding portion surrounding the light-transmissive portion; performing a plurality of exposures of a photoresist layer disposed on a substrate in a step-and-repeat-manner using the exposure mask, so as to form a plurality of inner projected parts corresponding to the inner light-shielding portions, the inner projected parts being aligned in a lattice as a whole; developing the photoresist layer on which the plurality of exposures have been performed; and etching the substrate using the developed photoresist layer as a mask.