With the widespread global application of BeiDou navigation, BeiDou B1C signaling based on Quadrature Multiplexed Binary Offset Carrier (QMBOC) modulation is expected to be extensively used in urban environments due to its wider signal bandwidth, smaller code pseudorange measurement errors, and stronger multipath capabilities. Despite offering higher positioning accuracy and secondary modulation characteristics of the BeiDou, B1C signals introduce the challenge of multiple peaks in the autocorrelation function. This leads to phase ambiguity during signal acquisition and tracking, resulting in positioning deviations of tens or even hundreds of meters. In urban environments, such deviations give rise to significant practical application issues. To address this problem, we have designed a multi-loop structure for the synchronous tracking of B1C signals and proposed a multi-peak phase-deblurring algorithm specifically tailored for the BeiDou B1C signal in urban environments. This algorithm considers the coupling relationship between the code and the carrier loops, and by matching the structural design of multiple loops, it achieves a precise and unambiguous phase estimation of the pseudocode, enabling the stable tracking of the entire loop for the BeiDou B1C signal. Simulation and actual testing demonstrate that the algorithm exhibits an error less than 0.03 for chip intervals when the signal-to-noise ratio is greater than −20 dB. Additionally, the accuracy can be improved by adjusting the set conditions, making it suitable for urban environments.