The autocorrelation function (ACF) of the Binary Offset Carrier modulation (BOC) signal for Global Navigation Satellite System (GNSS) has multiple peaks, ambiguity is easily generated during the synchronization of the baseband signal. Some methods have been proposed to remove the ambiguity, but the performance is not suitable for high-order BOC signals or does not maintain narrow correlation characteristics. This paper proposes a sub-function reconstruction synchronization algorithm to solve this problem, of which the key is to design a new local auxiliary code: the local Pseudo-Random Noise (PRN) code is divided into several new codes with different delays. The auxiliary code performs a coherent integration operation with the received signal. Then, a correlation function without any positive side peaks is obtained by multiplying the two correlation results to make the acquisition/tracking completely unambiguous. The paper gives a design scheme of navigation signal acquisition/tracking and deduces the theoretical analysis of detection performance. The phase discrimination function is provided. The performance of the method is analyzed from both theoretical and simulation aspects. Compared with the Binary phase shift keying-like (BPSK-LIKE) method, Subcarrier Phase Cancellation (SCPC) method and the Autocorrelation Side-Peak Cancellation Technique (ASPeCT) method, the proposed method has the best detection probability for the acquisition, which is 0.5 dB-Hz better than ASPeCT. For tracking, the proposed method performs best in terms of phase-detection curve, anti-multipath performance, and anti-noise performance. For high-order BOC signals, the SRSA technique successfully removes the false lock points, and there is only one multipath error envelope, and the code tracking error is almost the same as the ASPeCT method.