The invention provides a heterogeneous microphone automatic gain calibration method and system. The method comprises the following steps: acquiring a microphone signal, performing channel noise estimation on the signal, calculating a noise suppression control factor and correcting the signal to obtain a first target signal; performing reverberation estimation on the first target signal, calculating a reverberation control factor and correcting the first target signal to obtain a second target signal; and performing gain control on the second target signal to obtain a third target signal. The method and system can effectively suppress the channel noise without causing excessive distortion to the target signal, and repair the harmonic structure to avoid signal distortion, may adaptively estimate the reverberation time, ensure the accuracy of the reverberation suppression, accurately restore frequency band signals by calculating the amplitude gain in each frequency band, and avoids a defect that same-proportion expansion is achieved but the signal resolution in each band is not improved.