The object of the invention is to provide a method for manufacturing an SOI layer which is devoid of damages, has a reduced variation in thickness, and is uniform in thickness. The object is met by providing a method for manufacturing an SOI substrate comprising the steps of forming an oxide film at least on one surface of a first silicon substrate, implanting hydrogen ions from the surface of the first silicon substrate thereby forming an ion-implantation zone in the interior of the first silicon substrate, bonding the first silicon substrate over a second silicon substrate with the oxide film interposed thereby forming a laminated assembly, subjecting the laminated assembly to a first heating treatment consisting of heating at a specified temperature, so that the first silicon substrate is split at the ion-implantation zone thereby manufacturing a bonded substrate, flattening the exposed surface of the SOI layer by subjecting the bonded substrate to wet etching, subjecting the bonded substrate to a second heating treatment consisting of heating at 750 to 900° C. in an oxidative atmosphere thereby reducing damages inflicted to the SOI layer, and subjecting the resulting bonded substrate to a third heating treatment consisting of heating at 900 to 1200° C. thereby enhancing the bonding strength of the bonded substrate.