A method for manufacturing a bonded wafer includes: an ion implantation step of using a batch type ion implanter; a bonding step of bonding an ion implanted surface of a bond wafer to a surface of a base wafer directly or through an insulator film; and a delamination step of delaminating the bond wafer at an ion implanted layer, thereby manufacturing a bonded wafer having a thin film on the base wafer, wherein the ion implantation into the bond wafer carried out at the ion implantation step is divided into a plurality of processes, the bond wafer is rotated on its own axis a predetermined rotation angle after each ion implantation, and the next ion implantation is carried out at an arrangement position obtained by the rotation.