In view of the large workload and low efficiency in precisely determining pseudo-range jump time in the two-way ranging time synchronization of the navigation system, a method for rapid determination of pseudo-range jump based on clock drift rate estimation and binary search was proposed. The method took advantage of the property that the drift rate of on-board atomic clock is relatively stable over a long period of time. Firstly, the correct clock drift rate was calculated from the uplink and downlink pseudo-ranges according to the pseudo-range observing equations. Afterwards, the potential time period during which jump occurred was divided equally, producing two sub time periods. Two clock drift rate values and two jump quantities were solved respectively from the pseudo-range data of the above two sub time periods, and the next potential time period was the one with the larger jump quantity. The above procedure was repeated until the final potential time period was short enough. Finally, the precise jump time was determined by difference with the data in the final potential time period. Experimental results illustrate the correctness and effectiveness of the proposed method.