The invention discloses a method for suppressing the frequency doubling vibration force of a magnetically suspended flywheel based on an improved multi-resonant controller. The influence of rotor frequency doubling vibration force caused by a sensor error is considered, a dynamics model including frequency doubling vibration force is established for a magnetically suspended rotor, then the improved multi-resonant controller based on phase compensation is designed, compensation phase is introduced to adjust system stability when the multi-resonant controller is embedded into a basic control system, the multi-resonant controller parameter adjustment at each resonant frequency is based on a previous stable closed-loop control system, and the stability of the whole system is ensured and the complexity of parameter calculation is reduced by using a progressive parameter design. Through the above method, a suppression effect of frequency doubling current disturbance in a wide rotation speed range can be obtained with high accuracy and stability, thus the frequency doubling vibration force can be effectively suppressed, and the method has reference significance for the active vibration control of a magnetic bearing system.