In high frequency (HF) communication, M-ary frequency shift keying (MFSK) is a common modulation mode. The symbol rate estimation of MFSK signal is meaningful for the non-coo peration receiving. According to the analysis of channel distu rbance effect on signals, an algorithm is proposed to estimate the symbol rat e of MFSK signal. By means of extracting and filtering wavelet bridge, clust ering the distance of zero crossing, the effect of multi path and Doppler phenomenon in the symbol rate estimation can be overcome. Simulation experime nts show that the algorithm can reach a good accuracy degree when the channel is in low SNR and contains the multi path and Doppler effect. And it can be used for practical engineering.