Abstract: The issue of poor error-tolerance and polynomial taps restriction of Walsh Hadamard Transform (WHT) estimation method is studied and a novel soft fast PN sequence estimation algorithm based on weighting Walsh Hadamard Transform is proposed in this paper. Firstly, the theory analysis about error-tolerance likelihood bound of sequence hard-decision and restrictive factor of estimation polynomial taps is performed. Based on this analysis, the sequence soft information are taken to sequence frequency-coefficient to improve estimation performance, and the Walsh Hadamard matrix is column-weighted to change its binary property, which can decrease the polynomial taps influence to estimation performance. Meanwhile, the sequence control state are chosen to decease the estimation polynomial taps in the essence. The simulation results show that the proposed method is irrelevant with the order and tapped number of generator polynomial, and its performance is improved 1.5 dB than WHT.