To suppress an effect of metal contamination caused in manufacturing an SOI substrate. After forming a damaged region by irradiating a semiconductor substrate with hydrogen ions, the semiconductor substrate is bonded to a base substrate. Heat treatment is performed to cleave the semiconductor substrate; thus an SOI substrate is manufactured. Even if metal ions enter the semiconductor substrate together with the hydrogen ions in the step of hydrogen ion irradiation, the effect of metal contamination can be suppressed by the gettering process. Accordingly, the irradiation with hydrogen ions can be performed positively by an ion doping method.