A method for manufacturing bonded wafer including: producing bonded wafer having thin-film on its base wafer by an ion implantation delamination method, and reducing film thickness of the thin-film, wherein the step of reducing the film thickness includes a stage of reducing the film thickness by sacrificial oxidation treatment or vapor phase etching, wherein the method for manufacturing bonded wafer further includes a cleaning step of cleaning the bonded wafer exposing the delamination surface just before the step of reducing the film thickness, wherein the cleaning step includes a stage of performing a wet cleaning by successively dipping the bonded wafer to plural of cleaning baths, and wherein the wet cleaning is performed without applying ultrasonic in each of the cleaning baths in the wet cleaning. The method enables to clean bonded wafer exposing delamination surface remaining damage of ion implantation using a cleaning line in a strict control level.