In addition to provide an extremely clean environment for primary loop of high-temperature gas-cooled reactor (HTR), the primary helium circulator (PHC) using electromagnetic levitation technology also provides an effective means for vibration control. Besides synchronous vibration produced by mass imbalance and sensor runout, double-frequency vibration produced by unbalanced magnetic pull (UMP) is serious in PHC engineering prototype (PHC-EP). In this paper, we firstly analyzed the mechanism of UMP and the multi-frequency vibration characteristics in combination with the PHC-EP. Then we put forward a distributed iterative learning control (ILC) algorithm and a parallel control scheme to suppress the periodic vibrations. Finally, we verified the methods by carrying out experimental researches on the active magnetic bearing (AMB) bench of PHC-EP. The results show that the methods put forward in this paper have significant control effect on the double-frequency vibration generated by UMP of the PHC-EP, and provide theoretical and practical references for the PHC safe operation in HTR.