In order to capture the B1C navigation signal with BOC modulation, a specific acquisition scheme of PCO+FFT was proposed. Firstly, based on in-depth analysis of the characteristics of B1C signal, the segment length and FFT points were selected. Secondly, the algorithm was derived from coherent integral gain, uncorrelated integral gain, Doppler frequency measurement range and resolution, and detection probability. Thirdly, the FPGA implementation scheme based on the algorithm was given. Finally, the simulation performance of the algorithm was given to illustrate the effectiveness of the algorithm. The correctness of the implementation scheme is verified by the actual measurement on the FPGA hardware platform. The method of sub carrier separation and the realization of control core based on state machine have certain reference value for the improvement of navigation signal acquisition algorithm.