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Stability is a key problem that means whether a high rate rotor-active magnetic bearings system works reliably or not. Aiming at a bearings system described with nonlinear equations, this paper built a linear model according to the system behavior. Considering realization of the control system and behavior of a high rate rotor system (magnetic force is far smaller than input force produced by mass eccentricity) this paper proposes a design method of variable parameters PD control algorithm that can be used universally. The control system was simplified and a mass of adjusting work of control parameters was reduced. Analysis and simulation indicated that the bearings system could get a wider stable region of harmonic motion, and proved that the algorithm is robust and advanced. The control system can be realized because the winding electric currents are positive. The method is convenient for operation and can easily be used for engineering practice.