In this paper, the LEO system signal degradation is mainly due to fading and doppler shift, so that the analysis of the signal degradation and compensation techniques are very important. This paper propose a Kalman filter based two step Automatic Frequency Control(AFC) to combat large and time variant frequency offset in low earth orbit satellite communication systems. The proposed Kalman AFC method estimates a frequency offset in two steps, I. e., coarse and fine estimations, extending the frequency acquisition range to even for than the symbol rate. Furthermore, it can track well a time variation of frequency offset. It is shown that the proposed compensator is able to compensate for doppler shift more than several KHz.