The invention asks for protecting a modified smoothed pseudo Wigner-Ville distribution-based (MSPWVD-based) blind estimation method for a pseudo code sequence of a pseudo-random Bi-phase code-linear frequency modulation (PRBC-LFM) composite signal and belongs to the field of signal processing. According to the method, time-frequency analysis is performed on the PRBC-LFM composite signal by adopting modified smoothed pseudo Wigner-Ville distribution (MSPWVD), and thereby, the time-frequency concentration is enhanced while the cross-term interference of the signal is effectively reduced, and the precision of estimating the pseudo-noise (PN) code sequence of the PRBC-LFM composite signal is increased. Firstly, the minimum section of the MSPWVD time-frequency diagram of the signal is obtained from the MSPWVD time-frequency diagram of the signal; the phase jump site of an estimated pseudo code is obtained through detecting the peak position in the minimum section, and finally, the estimation on the original sequence or the antitone sequence of the PN code of the signal is obtained. Meanwhile, by combining with an MSPWVD-Hough transformation and subspace decomposition (singular value decomposition-SVD) method, the influences of cross terms are further reduced and the influence of the noise is further restrained. According to the method, the PN code sequence can be accurately estimated at low signal to noise ratio to successfully obtain the estimation on the parameter of the PN code of the PRBC-LFM composite signal, and thereby, the capacity of monitoring, managing, detecting and disturbing the PRBC-LFM composite signal and designing a related new-system system is improved. The MSPWVD-based blind estimation method for the pseudo code sequence of the PRBC-LFM composite signal has a wide application prospect.