The optimization purpose of a reservoir-and-pumping-station system in humid areas should be determining the optimal joint operation policy to reduce water spills of reservoirs, water replenishments of pumping stations, and meeting water demands. An optimization method for joint operation of a two-reservoir system with a series of pumping stations in humid areas is proposed in this paper. The method is based on dynamic programming and orthogonal test, and the dynamic programming is used to solve the subsystem models and orthogonal test is used to derive the joint operation policy between the subsystems, which can finally obtain the operation scheme both of the reservoirs and pumping stations. The proposed method was applied to the joint operation scheme of Shanhu Reservoir and Niqiao Reservoir with their sharing pumping stations in Liuhe District, Jiangsu Province, China. The results showed that the optimization method could reduce water replenishment of the system by 25.7% and save the operation time of pumping stations by 245 h in 2016, which reduced the operation cost.