Mirror-polished CZ wafer and FZ wafer are prepared. A first impurity region which will be a first isolation region is formed in a surface layer of a first main surface of the CZ wafer. The first main surface of the CZ wafer and a first main surface of the FZ wafer are bonded to each other by an inter-molecular bond. A second impurity region which will be a second isolation region is formed in a surface layer of a second main surface of the FZ wafer. A heat treatment is performed to diffuse the first impurity region and the second impurity region such that the first impurity region and the second impurity region are continuous, thereby forming a through silicon isolation region.