For the problem of the signal distortion of active sonar signal source output signal, a compensation method of signal source based on the wave filter was proposed. First the nonlinear transfer function of power amplifier was acquired. Then the wave filter was constructed via the nonlinear transfer function. Finally, the output signal source signal without distortion was corrected according to the wave filter. Theoretical analysis and experimental results show that, under the condition of this paper experimental, the method can effectively solve the problem of the signal distortion of active sonar signal source output signal, improve the robust of signal source output signal in active sonar, and the estimation accuracy of frequency bandwidth is improved more than 40%.