In view of the long running time of some mechanisms in the operation process of the Three Gorges ship lift and its influence on the operation efficiency of the ship lift，we carry out research on optimizing the operation process of the ship lift. According to statistical analysis and theoretical calculation，when the water level difference between the upstream and downstream channel is smaller than a certain range，the pipeline water pumping sequence affects the operational efficiency of the ship lift. In light of long-term operation and management experience，we propose an optimization plan for the pipeline water pumping process of the Three Gorges ship lift and conduct safety argumentation and efficiency analysis. The results show that under the existing conditions，the operation time of the ship lift is saved by about 70 s per compartment after process optimization，which greatly improves the operational efficiency of the ship lift.