A method of manufacturing an optical waveguide device includes providing an optical fiber guide for fixing an optical fiber and optical element placing portions for providing element mounting benches outside a waveguide fixing region of a silicon substrate. A metallic thin film is formed outside the waveguide fixing region of the silicon substrate. After an optical waveguide substrate is bonded to a whole of an upper surface of the silicon substrate through a bonding resin which will become an upper cladding layer, the optical waveguide substrate is diced along an edge of the waveguide fixing region, and the optical waveguide substrate outside the waveguide fixing region is removed to expose the optical fiber guide and the optical element placing portions.