Abstract The operation of a long-distance water diversion system in the transient process is a rather complicated problem requiring the joint operation of multiple devices. In this study, the joint operation of multiple hydraulic devices in the pumps shutdown process is expressed as a multi-objective optimization problem, and the hydraulic simulation-optimization model is proposed. The model is a bi-level framework, where the optimization model comprehensively considering various safety risks and efficiency through three objective functions is coupled with the MOC-based hydraulic transient simulation model. The parallel NSGA-II approach is proposed to solve the model. Besides, a process for effectively handling the constraints of the joint optimal operation of multiple hydraulic devices is proposed. Finally, the proposed model and approach are applied to a real long-distance water diversion project. The results show that the proposed model can find a set of feasible Pareto front solutions. The parallel approach greatly improves the computational efficiency. For the Pareto front schemes, the hydraulic devices are adjusted less frequently and the total regulation time is only 1/8.92–1/11.49 of that of the current operation scheme. Thus, this study provides an effective approach to formulate the joint operation scheme of multiple devices of long-distance water diversion systems.