A method of manufacturing an SOI wafer, including (a) forming a thermal oxide film on an SOI layer of an SOI wafer by a heat treatment under an oxidizing gas atmosphere, (b) measuring thickness of the SOI layer after forming the thermal oxide film, (c) performing a batch cleaning, wherein an etching amount of SOI layer is adjusted depending on thickness of the SOI layer measured in step (b) such that thickness of the SOI layer is adjusted to be thicker than a target value after etching, (d) measuring thickness of the SOI layer after batch cleaning, (e) performing a single-wafer cleaning, wherein an etching amount of the SOI layer is adjusted depending on thickness of the SOI layer measured in step (d) such that thickness of the SOI layer is adjusted to be the target value after etching, and removing the thermal oxide film formed in step (a) before or after step (b).