The invention discloses a method for controlling the wafer ion implantation dosage. The hardware comprises an ion beam (1), a wafer (2), a target disk (3), a closed-loop Faraday cup (4), an X-Tilt motor (5), a target platform (6), a linear motor (8), a PMAC controller (9), and a vacuum target chamber (10). In order to reduce particle impurities, process of ion implantation is carried out in the vacuum target chamber. The beam is generated by an ion source, and the processed ion beam (1) should meet requirements in uniformity and parallelism in order to arrive at the target chamber. According to process requirements, an included angle is reserved between the wafer (2) and the vertical direction. The linear motor (8) drives an air bearing to move up and down, and the wafer is ensured to move at constant speed when passing through a beam area. The implantation dosage at a single time and the total number N of scanning times are coordinated, and the N is an even number. According to the method, the scanning speed and the total number of scanning times of the motor are controlled through controlling the implantation dosage at a single time, thereby realizing purposes of being accurate in implantation dosage and improving the dosage uniformity.