A method for manufacturing a bonded wafer, includes: ion-implanting a gas ion such as a hydrogen ion from a surface of a bond wafer, thereby forming an ion-implanted layer; bonding the bond wafer and a base wafer; producing a bonded wafer having a thin-film on the base wafer by delaminating the bond wafer along the ion-implanted layer; and performing an RTA treatment on the bonded wafer in a hydrogen gas-containing atmosphere; wherein a protective film is formed onto the surface of the thin-film in a heat treatment furnace in the course of temperature-falling from the maximum temperature of the RTA treatment before the bonded wafer is taken out from the heat treatment furnace; and then the bonded wafer with the protective film being formed thereon is taken out from the heat treatment furnace, and is then cleaned with a cleaning liquid which can etch the protective film and the thin-film.