An SOI substrate which has a thick SOI layer is first prepared. Then, the SOI layer is thinned to a target film thickness using as a unit a predetermined thickness not more than that of one lattice. This thinning is performed by repeating a unit thinning step which includes an oxidation step of oxidizing the surface of the SOI layer by the predetermined thickness not more than that of one lattice and a removal step of selectively removing silicon oxide formed by the oxidation. The SOI layer of the SOI substrate is chemically etched by supplying a chemical solution to the SOI layer, and the film thickness of the etched SOI layer is measured. When the measured film thickness of the SOI layer has a predetermined value, a process of chemically etching the SOI layer ends.