To provide a method for manufacturing an SOI substrate provided with a single-crystal semiconductor layer which is suitable for practical use even when a substrate of which heat-resistant temperature is low, such as a glass substrate, is used, and to manufacture a highly reliable semiconductor device using such an SOI substrate. A semiconductor layer, which is separated from a semiconductor substrate and bonded to a supporting substrate having an insulating surface, is heated by supplying high energy by using at least one kind of particles having the high energy, and polishing treatment is performed on the heated surface of the semiconductor layer. At least part of a region of the semiconductor layer can be melted by the heat treatment by supplying high energy to reduce crystal defects in the semiconductor layer. Further, the surface of the semiconductor layer can be polished and planarized by the polishing treatment.