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With the advances of high strength/light weight composite material, high performance magnetic bearings, and power electronics technology, flywheel energy storage systems (FESS) are becoming an exciting alternative to traditional battery systems. One of the challenging problems of the FESS is to stabilize the rotor which is very sensitive to outside disturbances and plant uncertainties. In this paper, a stabilizing synchronization design of the FESS is proposed by incorporating cross-coupling technology into the optimal control architecture, which can be decomposed into two problems: a robust optimal control problem to improve the synchronization performance of the rotor in the radial directions and a stability problem. The control scheme is based on minimization of a new quadratic performance index in which the synchronization errors are embedded. Stability of the control scheme is investigated through linear quadratic Gaussian (LQG) optimal control technique. It is shown that with adequate control parameters the resulting control system can provide satisfactory synchronization performance, and the closed-loop stability can be guaranteed theoretically. Simulations on a compact and efficient flywheel energy storage system with integrated magnetic bearings demonstrate that the proposed approach is very effective to recover the unstable system when outside disturbances are present.