Provided is a method for manufacturing a bonded wafer with a good thin film over the entire substrate surface, especially in the vicinity of the lamination terminal point. The method for manufacturing a bonded wafer comprises at least the following steps of: forming an ion-implanted region by implanting a hydrogen ion or a rare gas ion, or the both types of ions from a surface of a first substrate which is a semiconductor substrate; subjecting at least one of an ion-implanted surface of the first substrate and a surface of a second substrate to be attached to a surface activation treatment; laminating the ion-implanted surface of the first substrate and the surface of the second substrate in an atmosphere with a humidity of 30% or less and/or a moisture content of 6 g/m3 or less; and a splitting the first substrate at the ion-implanted region so as to reduce thickness of the first substrate, thereby manufacturing a bonded wafer with a thin film on the second substrate.