The present study is based on the application of an interval two-stage stochastic programming (ITSP) model in the Yinma River Basin. A robust method based on interval two-stage robust (ITSR) optimization is introduced to construct an optimization model of water resource distribution in order to solve the problems of water shortage in low-income and high-income areas caused by the unreasonable distribution of water resources. The model would help in reducing the system risk in the Yinma River Basin caused by an excessive pursuit of economic benefits. The model simulations show that the amount of water required for the water resource distribution is significantly reduced after balancing the risks and the water resource distribution of the water use departments is reduced by up to 20%. In addition, the situation of water scarcity of various water use departments shows a decreasing trend. There is no scarcity of water use in Panshi, Yongji, Shuangyang and Jiutai areas. The water shortage of water use departments in other areas is reduced by up to 97%. The allocation of reused water to ecological and environmental departments with higher water demand further solved the water shortage problem in low-income departments in the interval-two-stage planning model. In this study, after the introduction of the robust optimization method in the Yinma River Basin, the stability of the water resources distribution system is significantly improved. In addition, the risk of water use system in the interval-two-stage stochastic model can be avoided.