A method of manufacturing a silicon-on-insulator (SOI) substrate is provided. The method includes forming an island-shaped insulating layer on a first surface of a first semiconductor substrate in a first region, forming a silicon epitaxial layer on the first surface of the first semiconductor substrate so as to cover the island-shaped insulating layer, forming a trench by etching the silicon epitaxial layer so as to expose the island-shaped insulating layer, and forming a first insulating adhesive layer on the silicon epitaxial layer and the island-shaped insulating layer so as to fill the trench.