Abstract: Active magnetic bearing rotor system has the characteristics that it can design targeted control strategy according to the performance index and operation characteristics of the rotor. It has particularly significant advantages in high-speed and high-power application scenarios. High speed permanent magnet motor has also been widely used in various fields because of its high power density and high efficiency. How to reduce the influence of the motor on the transmission force of the external structure is a key problem that must be solved in some special applications. In this paper, the current control strategy and transfer force control strategy based on iterative learning control method are designed to solve the problem of external transfer force suppression of large electromagnetic bearing rotor system under high speed operation. The current control strategy can eliminate the same frequency current stiffness force which accounts for the majority of the transfer force, while the transfer force control strategy can further achieve the overall suppression effect of the transfer force between the stator and rotor on the basis of the current control strategy. The theoretical and experimental results show that the designed transfer force control strategy can effectively suppress the transfer force amplitude between the stator and rotor under the high-speed operation condition of the large-scale AMB rotor system, so that the outward transfer energy of the motor is significantly reduced.