The carrier phase (CP) technique based on the BeiDou Global Satellite Navigation System (BDS-3) has proven to be a crucial spatial tool for remote time and frequency transfer. The current CP technique models the receiver clock offset as a white noise stochastic process and easily absorbs some unmodeled errors, thus compromising the time and frequency transfer performance. To further improve the performance of time and frequency transfer, a new BDS-3 receiver clock estimation algorithm based on the epoch difference (ED) model is presented, and the mathematical principles and applied modes are discussed. The algorithm makes full use of both observations of the current epoch and practical variations of the receiver clock offset, further improving the performance of time and frequency transfer. Five Multi-Global Navigation Satellite System Experiment network stations equipped with various types of receivers and antennas with dual-frequency BDS-3 signals were used to establish four time transfer links (i.e., AMC4–PTBB, BRUX–PTBB, OP71–PTBB, and WTZS–PTBB) to evaluate their effectiveness. The ED model improves all the four time links in terms of noise level, with improvements of 17.0%, 18.3%, 20.3%, and 5.9%, respectively, when compared with the results from a non-ED model. The ED model outputs were better than the raw solutions in terms of frequency stability at all time links, particularly for average time intervals (tau) < 1000 s. The mean improvement was 8.1% for AMC4–PTBB, 16.1% for BRUX–PTBB, 10.0% for OP71–PTBB, and 18.6% for WTZS–PTBB when the average time (tau) was less than 1000 s.
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