A method of manufacturing an optoelectronic composite substrate, includes forming a first cladding layer in an area except the connection pad on a wiring substrate including a connection pad on an upper surface, forming a belt-like core layer on the first cladding layer, and obtaining an optical waveguide having a structure in which the core layer is surrounded by the first cladding layer and the second cladding layer, by forming a second cladding layer which covers the core layer. A thickness of the first cladding layer is set identically to a thickness of the connection pad, and thus a level difference caused by the connection pad is eliminated.