Active magnetic bearings are widely used in the flywheel energy storage system because of their unique advantages. The limited-bandwidth and nonlinear behavior of the magnetic actuator with active magnetic bearings may cause instability for the system. Therefore, this paper proposes a modified proportional-resonant controller for regulating current and improving the stability in the full speed range. The design and optimization of the modified controller is investigated. Finally, experimental studies are carried out on the prototype of the magnetically suspended flywheel. The proposed controller is proved to be feasible and effective.