Binary offset carrier (BOC) modulation is a new modulation method that has been gradually applied to the Global Satellite Navigation System (GNSS) in recent years. However, due to the multi-peaks in its auto-correlation function (ACF), it will incur a false lock and generate synchronization ambiguous potentially. In this paper, an unambiguous synchronization method based on a reconstructed correlation function is proposed to solve the ambiguity problem. First, through the shape code vector constructed in this paper, the general cross-correlation function (CCF) expression of the BOC modulated signal will be obtained. Based on the features of the signal correlation function, it is decomposed into a matrix form of trigonometric functions. Then, it generates two local signal waves using a specific method, then the proposed method is implemented to obtain a no-side-peak correlation function by reconstructing the cross-correlation between the received signal and the two local signals. Simulations showed that it fully eliminates the side-peak threat and significantly removes the ambiguity during the synchronization of the BOC signals. This paper also gives the improved structure of acquisition and tracking. The detailed theoretical deduction of detection probability and code tracking error is demonstrated, and the corresponding phase discrimination function is given. In terms of de-blurring ability and detection probability performance, the proposed method outperformed other conventional approaches. The tracking performance was superior to the comparison methods and the phase discrimination curve only had a zero-crossing, which successfully removed the false lock points. In addition, in multipath mitigation, it outperformed the ACF of the BOC signal, and performs as well as the autocorrelation side-peak cancellation technique (ASPeCT) for BOC(kn,n) signals.