The present invention is a method for manufacturing a bonded wafer by an ion implantation delamination method including at least the steps of, bonding a bond wafer having a micro bubble layer formed by gas ion implantation with a base wafer to be a supporting substrate, delaminating the bond wafer along the micro bubble layer as a boundary to form a thin film on the base wafer, the method comprising, cleaning the bonded wafer after delaminating the bond wafer using ozone water; performing rapid thermal anneal process under a hydrogen containing atmosphere; forming a thermal oxide film on a surface layer of the bonded wafer by subjecting to heat treatment under an oxidizing gas atmosphere and removing the thermal oxide film; subjecting to heat treatment under a non-oxidizing gas atmosphere. As a result, the method for manufacturing a bonded wafer, which can remove the damage caused by the ion implantation and can suppress a occurrence of the concave defects without deterioration of surface roughness on the surface of the thin film of the bonded wafer after delamination is provided.