PROBLEM TO BE SOLVED: To provide a manufacturing method of a heterogeneous SOI substrate with an oxide film in which the density of defects with diameters of 0.5 μm or more on the oxide film is equal to or less than 7/cmand thus a surface defect is improved.SOLUTION: The heterogeneous SOI substrate includes a semiconductor thin film of a material different from that of a base substrate on the base substrate and has an oxide film on a surface of the semiconductor thin film. The manufacturing method of the heterogeneous SOI substrate with the oxide film includes at least the steps of: etching the heterogeneous SOI substrate at least twice by using fluorine containing solutions with different etching rates to remove the oxide film; and performing thermal processing on the etched heterogeneous SOI substrate under the presence of oxygen to form the oxide film on the etched surface of the semiconductor thin film. The density of defects with diameters 0.5 μm or more on the surface of the semiconductor thin fil
