Aiming at the problem of ambiguous synchronization of binary offset carriers due to sub-peaks, a sub-peak elimination technique based on overlapping sub-correlation functions is proposed. In this algorithm, the correlation function model without the main peak is constructed, the concept of overlapping sub-correlation function is proposed, and the function at each sub-peak point is given by combining the sub-correlation function. The sub-peak elimination technique based on overlapping sub-correlation function is compared with ASPeCT and SCPC in simulation experiments, and the results show that the proposed algorithm has a higher acquisition probability under the same signal-to-noise ratio condition. In terms of tracking, there are no mis-locked points, the discrimination slope is maintained at a high level and improved by 1 dB, and the multipath error envelope area was reduced by 10%.