A method of manufacturing a silicon-on-insulator substrate, comprising the steps of: irradiating one surface of a semiconductor substrate with ions to form an embrittlement layer at a given depth from the one surface of the semiconductor substrate; forming an insulating layer over the one surface of the semiconductor substrate or over a supporting substrate after or before the irradiation process; performing a heat treatment for generating a crack in the embrittlement layer in a state that the semiconductor substrate and the supporting substrate are overlapped with each other with the insulating layer interposed therebetween and for separating the semiconductor substrate at the embrittlement layer so that a semiconductor layer is formed over the supporting substrate; and performing a first polishing treatment or an etching treatment on a surface of the semiconductor layer such that uniform heat capacity of the semiconductor layer can be obtained in a following irradiation step comprising irradiating the semiconductor layer which is subjected to the first polishing treatment with an electromagnetic wave such that at least part of the semiconductor layer is melted by irradiation with the electromagnetic wave thereby reducing a crystal defect in the semiconductor layer by recrystallization; the method further characterized in that performing a second polishing treatment on the surface of the semiconductor layer after irradiating the semiconductor layer; and the irradiation step is first performed with fluorine ions and then irradiation is performed with hydrogen ions, and when hydrogen is used as a source gas, H 2 + ions and H 3 + ions are used as main ions for irradiation. irradiating one surface of a semiconductor substrate with ions to form an embrittlement layer at a given depth from the one surface of the semiconductor substrate; forming an insulating layer over the one surface of the semiconductor substrate or over a supporting substrate after or before the irradiation process; performing a heat treatment for generating a crack in the embrittlement layer in a state that the semiconductor substrate and the supporting substrate are overlapped with each other with the insulating layer interposed therebetween and for separating the semiconductor substrate at the embrittlement layer so that a semiconductor layer is formed over the supporting substrate; and performing a first polishing treatment or an etching treatment on a surface of the semiconductor layer such that uniform heat capacity of the semiconductor layer can be obtained in a following irradiation step comprising irradiating the semiconductor layer which is subjected to the first polishing treatment with an electromagnetic wave such that at least part of the semiconductor layer is melted by irradiation with the electromagnetic wave thereby reducing a crystal defect in the semiconductor layer by recrystallization; the method further characterized in that performing a second polishing treatment on the surface of the semiconductor layer after irradiating the semiconductor layer; and the irradiation step is first performed with fluorine ions and then irradiation is performed with hydrogen ions, and when hydrogen is used as a source gas, H 2 + ions and H 3 + ions are used as main ions for irradiation.