In order to address the ambiguous synchronization problem caused by the multi-peak nature of the autocorrelation function of the modulated signal of the Multiplexed Binary Offset Carrier (MBOC) in the Global Navigation Satellite System (GNSS), a new synchronization algorithm for MBOC signals is presented in this paper, which uses a reconstruction correlation function to effectively handle synchronization ambiguities associated with multi-peak signals. The paper proposes an algorithm for reconstructing the correlation function of the MBOC signal by analyzing its characteristics. The algorithm generates three local auxiliary signals, namely, pseudo-random codes (PRN), BOC(1,1) signals, and MBOC signals, which are correlated with the received signal. By combining the three correlation functions, the algorithm produces a reconstructed correlation function based on reconstruction rules, eliminating side peaks and achieving unambiguous synchronization. Simulation results show that the proposed algorithm in this paper eliminates all side peaks while maintaining a high detection probability, and its deblurring capability is optimal compared to other algorithms. In addition, the discriminant curve shows that the algorithm in this paper successfully eliminates all the mis-locked points, and the slope gain is improved by more than 2.5 dB compared with other algorithms, and the anti-multipath performance of the algorithm in this paper is better than that of other traditional algorithms, such as ASPeCT (Autocorrelation Side-Peak Cancellation Technique).