Large Doppler shifts are inherent to high-speed relative motion between receiver and satellite and are likely to cause major problems during the code phase acquisition due to the introduced frequency ambiguity. In order to solve the problem of acquisition for the binary offset carrier (BOC) modulated the signal with large Doppler shift, a novel acquisition algorithm based on partial matched filter-all phase fast Fourier transform (PMF-apFFT) is proposed in this paper. In this method, all phase processing was adopted to weaken the effect of spectrum leakage after partial correlation, and two dimensional parallel searching for Doppler frequency on different code phases was completed by the maximum value after the cumulative average exceeding the threshold. The theoretical analysis and simulation results show that the correct code phase search and high precision estimation of Doppler frequency can be completed by the proposed algorithm at the same time. Compared with the traditional PMF-FFT acquisition algorithm, the proposed algorithm has stronger anti-noise performance and a better detection probability, and it is suitable for the complex communication environment of strong noise and large Doppler shift.INDEX TERMS Partial matched filter-all phase fast Fourier transform (PMF-apFFT), binary offset carrier (BOC) signal, acquisition, large Doppler shift.