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The FPGA-based radial controller of a four-axis Magnetic bearing to meet the need of momentum flywheels for attitude control system of spacecraft is designed. The control strategy involves decentralized PD control, cross feedback control and generalized notch filter. The decentralized PD and cross feedback control strategy is implemented by distribution of poles and zeros of the compensator; the generalized notch filter is designed based on coordinate transformations. In the FPGA implementation of the controller, the floating-point IP core is used to implement the combined control algorithm and the method of repeat utilization of the logic resources is adopted. Only 150,000 equivalent logic gates are used. The experiment results show that the performance of the controller is satisfying.