The dual-estimate method has been proposed to solve the ambiguous tracking problem for binary offset carrier (BOC) modulated signals in global navigation satellite system. In order to improve the anti-multipath performance of the dual-estimate method, the local generated pseudo-random code is designed to be bipolar zero-return code which appears at each edge of the code chip. Herein the obtained two-dimensional correlation function would get a sharper correlation peak, and the dual-estimate method would get a stronger anti-multipath performance. The anti-multipath performance is analyzed in the band limited condition theoretically, then a simulation experiment is also given. The result shows that the proposed method can achieve an unambiguous, anti-multipath and anti-low carrier-to-noise ratio estimation for BOC modulated signals compared with the existing methods.