As one of the key technologies of high-temperature gas-cooled reactor, primary helium circulator–equipped active magnetic bearing provides driving force for primary helium cooling system. However, repetitive periodic vibration produced by rotor imbalance may introduce risks to primary helium circulator (even for high-temperature gas-cooled reactors). First, this article analyzes a periodic component extraction algorithm which is widely used in active magnetic bearing rotor unbalance control methods and points out the problem that the periodic component extraction algorithm occupies numerous computing resources which cannot satisfy the real-time request of active magnetic bearing control system. Then, a novel iterative learning control algorithm based on the iteration before last iteration of system information (iterative learning control-2) and a plug-in parallel control mechanism based on the existing control system are put forward, meanwhile, an integrated independent distributed active magnetic bearing control system is designed to solve the problem. Finally, both the simulation and experiment are carried out, respectively. The corresponding results show that the control method and control system proposed in this article have significant suppression effect on the repetitive periodic vibration of the active magnetic bearing system without degrading the real-time requirement and can provide important technical support for the safe and stable operation of the primary helium circulator in high-temperature gas-cooled reactor.