The high accuracy calibration method for the system characteristics of geophysical prospecting instruments based on correlation identification is proposed in this paper.The inverse repeated M sequence is used as the excitation signal, the measurement channel of the instrument is disturbed with encoded input current, the excitation current and instrument response output in time series is recorded according to the same sampling rate, and then circular cross-correlation method is used to obtain the instrument system frequency response.The simulation results show that the frequency resolution of the instrument system is improved by using the method based on encoding source, the multi-period excitation can significantly improve the accuracy of identification, and the right sampling rate is also helpful to improving the accuracy of identification, but it should match with the system data storage capacity.