In a method of manufacturing an optical device including an optical waveguide having a core, a cladding and a light input/output part through which a light beam is input or output, a substrate is prepared which is provided with a uniform thickness of single-crystalline film having its constituent atoms forming a diamond lattice structure and its surface being neither the (111) plane nor its equivalent planes. In the single-crystalline film, a precursor structure is formed which has a precursor of light input/output part. A mask is formed such as to expose the precursor with the remaining part covered. The structure is immersed into an alkaline solution for wet etching with the (111) planes used as etch-stop planes.