A method of manufacturing an optical device that includes a relief structure formation layer, a first layer made of a first material having a refractive index different from that of a material of the relief structure formation layer, and a second layer made of a second material different from the first material and covering the first layer. A ratio of an amount of the second material at a position of the second region to an apparatus area of the second region is zero or smaller than a ratio of an amount of the second material at the position of the second sub-region to an apparatus area of the second sub region.