The invention relates to MFSK water sound communication method and an MFSK water sound communication system. According to the method, m sequence is employed for digital signal modulation, after signal frequency spectrum broadening, the m sequence is modulated to a radio frequency signal, and the modulation radiofrequency signal is sent out; during signal demodulation, correlation operation of the m sequence and a reception signal is carried out, a peak initial position of each code element is estimated to realize code element synchronization, code element diffusion is then realized, then frequency estimation is carried out, a CZT transformation algorithm is employed for frequency estimation to realize frequency spectrum refinement for the frequency band signal after despreading, the refined frequency spectrum is acquired, channel decoding is carried out according to the refined frequency spectrum, output is carried out, the reception signal frequency spectrum is better refined, the smallest frequency interval is smaller, code element length requirements during frequency estimation are reduced, a communication rate is improved, the frequency interval is reduced, frequency utilization efficiency is improved, and code element synchronization processing is made to be more precise.