This paper suggests a compensating method of flux fluctuations in permanent magnet of AC servo system. after analyzing the characteristics and control measures of flux fluctuations, the compensation strategy for reducing the effect of flux fluctuations on electromagnetic torque is put forward. Though the simulation experiments it is shown that the flux compensation method for improving the position control accuracy of the movers when their running at high speed is proved to be positive effective. For CNC machine tools, industrial robots and other occasions involving sophisticated movement, synchronous servo motors in permanent magnet are usually driven by high-performance sine wave. In order to obtain good control performance, the high demands are put forward for reducing the torque fluctuations Torque fluctuations are an important factor to affect the stability of low speed servo drive system, high-speed stability and precision position control. There are many factors causing torque fluctuations, in which the flux fluctuations in permanent magnet are an important one.