M-Sequence, short for Maximum Linear Feedback Shift Register Sequence, is widely used in identification friend or foe (IFF) system because of its good equalization and autocorrelation characteristics, and Minimum Shift Keying (MSK) signal has been paid more attention in military communication field because of its excellent signal characteristics. A new demodulation method for MSK modulation signal of M-Sequence is studied. The MSK signal is sampled by A/D converter, and an integration circuit is designed in the FPGA. The same M-Sequence is generated by the same M-Sequence source polynomial as the integrator coefficient. The peak value of the integrated signal is judged to determine the M-Sequence. When the symbol rate is 1 Mbps and the carrier rate is 1 Mbps and M-Sequence is 5 bits, the recognition time of the new method is less than 1 us, which is less than one fifth of the recognition time of the traditional demodulation method. This method simplifies the demodulation process and is easy to implement. It improves the recognition speed of M-Sequence in MSK modulation signal and provides some reference value for the development of IFF system.