An object of the present invention is to provide a method for manufacturing an SOI substrate provided with a semiconductor layer which can be used practically even where a substrate having a low upper temperature limit such as a glass substrate is used. The manufacturing method compromises the steps of preparing a semiconductor substrate provided with a bonding layer formed on a surface thereof and a separation layer formed at a predetermined depth from the surface thereof, bonding the bonding layer to the base substrate having a distortion point of 700° C. or lower so that the semiconductor substrate and the base substrate face each other, and separating a part of the semiconductor substrate at the separation layer by heat treatment in order to form a single-crystal semiconductor layer over the base substrate. In the manufacturing method, a substrate which shrinks isotropically at least by the heat treatment is used as the base substrate.