Based on the diversity of the agricultural system, this research calculates the planting structures of rice, maize and soybean considering the optimal economic-social-ecological aspects. Then, based on the uncertainty and randomness of the water resources system, the interval two-stage stochastic programming method, which introduces the uncertainty of the interval number, is used to calculate the groundwater exploitation and the use efficiency of surface water. The method considers the minimum cost of water as the objective of the uncertainty model for surface water and groundwater joint scheduling optimization for different planting structures. Finally, by calculating harmonious entropy, the optimal exploitation utilization interval of surface water and groundwater is determined for optimal cultivation in the Sanjiang Plain. The optimal matching of the planting structure under the economic system is suitable when the mining ratio of the surface is in 44.13%–45.45% and the exploitation utilization of groundwater is in 54.82%–66.86%, the optimal planting structure under the social system is suitable when surface water mining ratio is in 47.84%–48.04% and the groundwater exploitation threshold is in 67.07%–72.00%. This article optimizes the economic-social-ecological-water system, which is important for the development of a water- and food-conserving society and providing a more accurate management environment.