It is an object to provide a method for manufacturing an SOI substrate in which crystal defects of a single crystal semiconductor layer are reduced even when a single crystal semiconductor substrate in which crystal defects exist is used. Such an SOI substrate can be manufactured through the steps of forming a single crystal semiconductor layer which has an extremely small number of defects over a single crystal semiconductor substrate by an epitaxial growth method; forming an oxide film on the single crystal semiconductor substrate by thermal oxidation treatment; introducing ions into the single crystal semiconductor substrate through the oxide film; bonding the single crystal semiconductor substrate into which the ions are introduced and a semiconductor substrate to each other; causing separation by heat treatment; and performing planarization treatment on the single crystal semiconductor layer provided over the semiconductor substrate.