Multistage irrigation pumping system is often faced with these typic problems of scarce water resource, high lift of water pumping, coexistence of different irrigation methods, difficult allocation of water, high cost of operation etc. It is significant to optimize the water regulation to alleviate above problems. A typical multistage irrigation pumping system (Guhai irrigation system) in Ningxia Hui Autonomous Region was taken as a case study area, and a regional multiobjective optimization model was developed with a twolevel hierarchical structure for optimal regulation of irrigation water. Water requirement and energy consumption were taken as two objectives in the model so as to consider the operations of pumping stations. Meanwhile, different irrigation periods were considered to obtain detailed schedules for water allocation and operation. Based on the decompositionharmonization method for large system, a twolevel structure was constructed to better describe the characteristics of multilevel and interrelated relationship, complicated structures and multiple impact factors. The first level dealt with the optimal allocation of irrigation water supply among various crops in each pumping station. The second level sought out the optimal schemes of pumping and allocating water among multistage pumping stations. Each level was solved independently, while they were coordinated through taking water supply amount as coordinating variables. Based on the optimization model, optimal schemes for water allocation and pumping station operation were presented for all stages of pumping stations under approved amount of water resources in the study area. Results indicated that the total water shortage amount was significantly 〖JP3〗reduced from 5.77×10 6m3 to 1.30×10 4m3 in the whole system, and it was reduced from -3.22×106~2.47×106m3 to -8.30×104~9.50×104m3 among each pumping station. The spatialtemporal contradictions of water supply among multistage pumping stations were effectively alleviated through the optimization of water supply. The research provided an effective and practicable tool to optimize the regional water allocation for complex multistage pumping irrigation system, and the model can be further practiced for actual water management.