Aiming at the optimal allocation of irrigation water in multi-water source project in water resource shortage area, this study developed a water resource joint scheduling optimization model for the reservoir and the pumping station under deficit irrigation conditions. In the model, the maximum annual yield of the irrigation area was the objective function; the water supply, water spill of the reservoir and replenishment water of the pump station at each stage as the decision variables; and the total annual water supply of the system, the reservoir operation criteria, the water rights of the pump station, and the water demand of the crop during the entire growth period were the constraint conditions. According to the characteristics of the model, a large system decomposition aggregation dynamic programming (DADP) method is proposed to transform N + 1 dimensional dynamic programming problem into N + 1 one-dimensional dynamic programming problem for solution. In addition, this study also uses real-coded genetic algorithm (RGA) and DADP to compare the algorithms, and discusses the performance of the two algorithms from the optimization of the algorithm and the applicability of the algorithm.