A method of producing a bonded wafer in which wafers each having a cutout portion are used as a bond wafer and a base wafer, and either or both of settings of an ion implanter with which ions are implanted and conditions of the ion implantation are adjusted in the step of implanting the ions such that a cutout portion of either or both of the bond wafer and the base wafer after bonding is located at within a range of 0±30° or 180±30° from a position at which separation of the bond wafer begins in the step of separating the bond wafer. This method can inhibit the occurrence of large fault defect that may be generated on a surface of a thin film right after the separation, when a thin film such as an SOI layer is formed by the ion implantation separation method.