A manufacturing method for manufacturing an SOI wafer by bonding a single crystal silicon wafer to a transparent insulation substrate, and thereafter making the single crystal silicon wafer to be thinned to form an SOI layer on the transparent insulation substrate, the manufacturing method performing at least: a step of preparing the single crystal silicon wafer and the transparent insulation substrate being one of a silica substrate and a sapphire (alumina) substrate; a step of forming an ion injection layer within the single crystal silicon wafer, by injecting at least one of a hydrogen ion and a rare gas ion from a surface of the single crystal silicon wafer with an ion injecting dose greater than 8,0x10 16 /cm 2; a step of processing the ion injection surface of the single crystal silicon wafer and/or a surface of the transparent insulation substrate, with a plasma processing, by placing the single crystal silicon wafer and/or the transparent insulation substrate in a vacuum chamber to which plasma gas is introduced in order for the single crystal silicon wafer and/or the transparent insulation substrate to be subjected to high frequency plasma or with an ozone processing, by placing the single crystal silicon wafer and/or the transparent insulation substrate in a chamber in which atmospheric air and one of a nitrogen gas or an argon gas are introduced and by generating high frequency plasma to convert oxygen in the atmospheric air into ozone; a step of bonding the ion injection surface of the single crystal silicon wafer to a surface of the transparent insulation substrate, by bringing them into contact with each other at room temperature, with the processed surface(s) as bonding surface(s); a step of raising a bonding strength by performing thermal processing to the bonded wafer under a temperature of 100-300 degrees centigrade and then, a step of obtaining an SOI wafer, by mechanically peeling the single crystal silicon wafer by giving an impact to the ion injection layer, to form an SOI layer on the transparent insulation substrate; a step of performing thermal processing for flattening a surface of the SOI layer, to the obtained SOI wafer, under an atmosphere of an inert gas, a hydrogen gas, or a mixture gas of the inert gas and the hydrogen gas; and then a step of polishing the surface of the SOI layer by removing a thickness equal to or smaller than 70nm from the surface of the SOI layer; after the step of polishing, a step of forming a thermal oxide layer on the surface of the SOI layer by performing thermal oxidation to the SOI wafer to which the thermal processing for flattening has been performed; and after the step of forming the thermal oxide layer, a step of reducing a thickness of the SOI layer by removing the thermal oxide layer. a step of preparing the single crystal silicon wafer and the transparent insulation substrate being one of a silica substrate and a sapphire (alumina) substrate; a step of forming an ion injection layer within the single crystal silicon wafer, by injecting at least one of a hydrogen ion and a rare gas ion from a surface of the single crystal silicon wafer with an ion injecting dose greater than 8,0x10 16 /cm 2; a step of processing the ion injection surface of the single crystal silicon wafer and/or a surface of the transparent insulation substrate, with a plasma processing, by placing the single crystal silicon wafer and/or the transparent insulation substrate in a vacuum chamber to which plasma gas is introduced in order for the single crystal silicon wafer and/or the transparent insulation substrate to be subjected to high frequency plasma or with an ozone processing, by placing the single crystal silicon wafer and/or the transparent insulation substrate in a chamber in which atmospheric air and one of a nitrogen gas or an argon gas are introduced and by generating high frequency plasma to convert oxygen in the atmospheric air into ozone; a step of bonding the ion injection surface of the single crystal silicon wafer to a surface of the transparent insulation substrate, by bringing them into contact with each other at room temperature, with the processed surface(s) as bonding surface(s); a step of raising a bonding strength by performing thermal processing to the bonded wafer under a temperature of 100-300 degrees centigrade and then, a step of obtaining an SOI wafer, by mechanically peeling the single crystal silicon wafer by giving an impact to the ion injection layer, to form an SOI layer on the transparent insulation substrate; a step of performing thermal processing for flattening a surface of the SOI layer, to the obtained SOI wafer, under an atmosphere of an inert gas, a hydrogen gas, or a mixture gas of the inert gas and the hydrogen gas; and then a step of polishing the surface of the SOI layer by removing a thickness equal to or smaller than 70nm from the surface of the SOI layer; after the step of polishing, a step of forming a thermal oxide layer on the surface of the SOI layer by performing thermal oxidation to the SOI wafer to which the thermal processing for flattening has been performed; and after the step of forming the thermal oxide layer, a step of reducing a thickness of the SOI layer by removing the thermal oxide layer.