In this paper, irrigation system optimization with limited water supplies efficiency of water application. A system optimization model was developed for crop irrigation system with the every irrigation quota as the decision variable. The model was based on a simulation model of the soil water balance and the crop water-production function, and was optimized by the elitist non-dominated sorting genetic algorithm (NSGA-II). NSGA-II is introduced to optimize irrigation system under the condition of non-sufficient irrigation. The result of example proves that the NSGA-II method is equal-distributing, fast-calculation, and the astringency and the robustness is nice to get the Pareto optimal solution in objective space.