In order to eliminate the vibration of Magnetically Suspended Flywheel(MSFW), the disturbing sources of MSFW are analyzed.Aimed at the suppression of main disturbing sources, the unbalance vibration, a new active vibration system based on TMS320C6713B+FPGA digital controller is presented. The active vibration control method, hardware constitution and functions of digital controller are discussed. The implement of control method in DSP, the organization of multi tasks in FPGA and the control of peripheral devices are provided. The experimental results demonstrate that the unbalance vibration has been reduced to 3.2％ by proposed system, which shows this system can eliminate the unbalance vibration of MSFW significantly and has great significance and value for increasing the stability of attitude control and for improving the resolution of earth observation.