In this study, an integrated agricultural water management system based on interval mixed two-stage stochastic programming (ITSP) has been applied to the long-term planning of water management activities in Yongxin County, Jiangxi Province, China. A conjunctive use of water system is structured for characterizing the developed model. The model can effectively reflect dynamic, interactive, and uncertain characteristics of the water management system in the area. Solutions of the model provide optimal water allocation patterns for decision makers. The results are helpful to address the conflicts existing between the water resources and socio-economic development.