For a water conveyance project that combined pressurization and gravity flow, it is difficult to balance the global safety problem only by controlling a single water facility. The issue of joint control of pumps and valves under continuous shutdown conditions was discussed. The shutdown interval between parallel pumps, the closing law of the pump discharge valves and the closing process of the terminal control valves were considered, and their impacts on the extreme water hammer pressure in the pipeline system and the water level in the high-elevated pool were analyzed. The joint control of pumps and valves optimization model was established, which was coupled with the hydraulic calculation method. A non-dominated sorting artificial rabbits optimization algorithm (NSARO) was proposed based on non-dominated sorting and crowding distance. The excellent convergence of the NSARO in the joint optimization and control of pumps and valves was verified by the hypervolume (HV) index. Grey relational analysis (GRA) was used to pinpoint the optimal scheme from the Pareto solution set. In the case of an actual project, the NSARO-GRA optimization solution decision-making method was used to obtain the optimal scheme. Compared with the current scheme, the maximum positive pressure head, maximum negative pressure head in the pipeline system, and water level fluctuation value in the high-elevated pool of the optimal scheme have been reduced by 13.57, 0.29 and 5.79 m, respectively.