Theperformanceoftheglobalnavigationsatellitesystem(GNSS)canbeenhancedsignificantly by introducing the inter-satellite links (ISL) of a navigation constellation. In particular, the improvement of the position, velocity, and time accuracy, and the realization of autonomous functions require the ISL distance measurement data as the original input. For building a high-performance ISL, the ranging consistency between navigation satellites becomes a crucial problem to be addressed. Considering the frequency aging drift and the relativistic effect of the navigation satellite, the frequency and phase adjustment (FPA) instructions for the 10.23 MHz must be injected from the ground station to ensure the time synchronization of the navigation constellation. Moreover, the uncertainty of the initial phase each time the onboard clock equipment boots also results in a pseudo-range offset. In this Ref., we focus on the influence of the frequency and phase characteristics of the onboard clock equipment on the ranging consistency of the ISL and propose a phase compensation sensor design method for the phase offset. The simulation and experimental results show that the proposed method not only realized a phase compensation for the pseudo-range jitter, but, when the 1 PPS (1 pulse per second) falls in the 10.23 MHz skip area, also overcomes the problem of compensating the ambiguous phase by directly tracking the 10.23 MHz to ensure consistency in the ranging.