Magnetically Suspended Flywheel (MSFW) is an actuator for the high precision attitude control of spacecrafts such as satellites.In order to improve the reliability and flexibility of a MSFW control system for space applications,a FPGA-based digital controller for Active Magnetic Bearing (AMB) is investigated. Firstly, the model of the magnetic bearing system is set up and several kinds of suitable control strategies are chosen. Then, by using the idea of on-chip hardware and software co-design, an AMB controller based on a FPGA and a LEON3 soft processor is presented,and a prototyping platform is built to test control algorithms and to verify the system performance. Finally, a self-repairing FPGA-based AMB controller is proposed. Comparing with the DSP-FPGA-based AMB controller, the FPGA-based controller has decreased the failure rate by 10% and the board area by 30%. Experimental results indicate that the beating of flywheel rotor and the torque output error are less than 20 μm and 4×10-3N·m,respectively, and the inconsistency between positive and inversion is less than 10% under the control of the FPGA-based AMB controller and the working speed scope of MSFW.These data prove that the proposed controller has achieved a higher precision.