This invention makes it possible to simplify a process of manufacturing an SOI substrate whose insulator is not exposed to the side surface. The SOI substrate manufacturing method includes a first step of forming a structure (230) in which an insulating layer (204b) and semiconductor layer (203b) are in turn formed on a semiconductor member (211) by bonding a first substrate (210) to a second substrate (220), a second step of making the edge portion of an insulating layer (204b) of the structure (230) retreat toward the center so that the edge portion of a semiconductor layer (203c) overhangs the edge portion of an insulating layer (204c), and a third step of moving atoms which form the edge portion of the semiconductor layer (203c) such that the edge portion of a semiconductor layer (203d) covers the periphery of the insulating layer (204c) and connects to the semiconductor member (211).