A method is demonstrated to manufacture SOI substrates with high throughput while resources can be effectively used. The present invention is characterized by the feature in which the following process A and process B are repeated. The process A includes irradiation of a surface of a semiconductor wafer with cluster ions to form a separation layer in the semiconductor wafer. The semiconductor wafer and a substrate having an insulating surface are then overlapped with each other and bonded, which is followed by thermal treatment to separate the semiconductor wafer at or around the separation layer. A separation wafer and an SOT substrate which has a crystalline semiconductor layer over the substrate having the insulating surface are simultaneously obtained by the process A. The process B includes treatment of the separation wafer for reusing, which allows the separation wafer to be successively subjected to the process A.