Synchrotron radiation‐assisted etching of SiO2 in a hydrogen atmosphere and its application to pretreating and cleaning substrates prior to Si film deposition is discussed. Thermally oxidized SiO2 film is etched in irradiation by synchrotron radiation at about 500 °C. Its etch rate increases by a factor of two in a hydrogen atmosphere. SiO2 core electron excitation by such irradiation seems to play an important role in SiO2 film modification and etching. This treatment reduced the interface contaminants such as oxygen and carbon between the deposited film and substrate to levels below the detection limit of secondary ion mass spectroscopy. Our results demonstrate that this new process is effective for low‐temperature treatment.