SNR (Signal to Noise Ratio) estimation is a very important parameter for channel estimation of the communication system. In this paper, some SNR estimation methods of digital modulation system are applied and improved in FM modulation system. Then we summarize several SNR estimation methods (EHM (Envelope High order Moment method), SE (Spectrum Estimation method), FD (Frequency Domain method), EMV (Envelope Mean Variance method), M2M4 (Second order and Fourth order Moment method)). Furthermore, according to the characteristics of FM modulation system, we put forward the improvement of M2M4 and also discuss the optimal algorithm for underwater acoustic Rayleigh channel, Rician channel and Bellhop channel by comparing these methods.