The invention discloses a method for correcting the coordinate mapping error during the process of polishing an ion beam, the method ingeniously utilizes the removing function test course during the process of polishing the ion beam, in the course, a plurality of removing function tests are carried out in different positions of an optical mirror at the same time, then the accurate positions of the centers of the removing functions on the optical mirror are found out, the position information and the position control information applied in the tests are utilized, the precise coordinate mappingbetween the coordinate system of the optical mirror and the coordinate system of a machine tool can be indirectly determined, thereby eliminating the influence of the coordinate mapping error in the traditional tool setting process to the processing. The method overcomes the problem that the coordinate mapping has errors through the simple and feasible method in the prior art, improves the machining accuracy during the process of polishing the ion beam, and provides the important technical guarantee for realizing the high-precision optical processing.