To suppress desorption of hydrogen ions with which a single crystal semiconductor substrate is irradiated. A method for manufacturing an SOI substrate includes the following steps: irradiating a semiconductor substrate with carbon ions; irradiating the semiconductor substrate with a hydrogen ion after the irradiation with the carbon ion so as to form an embrittled region in the semiconductor substrate; disposing a surface of the semiconductor substrate and a surface of a base substrate to face each other and to be in contact with each other so that the semiconductor substrate and the base substrate are bonded; and heating the semiconductor substrate and the base substrate which are bonded to each other and separating the semiconductor substrate along the embrittled region so that a semiconductor layer is formed over the base substrate.