Pumping wells (PWs) lie at the core of agricultural irrigation infrastructure, and their spatial configuration is of great significance for the scientific management of regional agriculture and rational use of water resources. To solve the problems of unreasonable and unscientific spatial allocation of regional agricultural irrigation PWs, this paper proposes a new strategy for updating agricultural irrigation PWs based on a spatial decision model, using Songzhuang Town, Tongzhou District, Beijing as a case study. The model utilizes constraints based on local factors such as actual land use, and proposes a novel feasible solution strategy that combines random local search and abrupt jumps to increase the probability that feasible solutions will be found, addressing the performance issues of simulated annealing algorithms, influence of initial values, and parameter sensitivity. Finally, we used the proposed method to perform updated decision analysis on the spatial configuration of PWs in the study area. The results showed that most of the crops in the study area lack irrigation, and the currently available PWs cannot meet the needs for irrigation. The new PWs added based on this decision method can be more evenly distributed within the predefined optimization unit. The proposed number of PWs to be added is 166, the density of PWs is 0.04/ha, and the crop area covered by the PWs is 3350.43 ha. In contrast to the previous PW layout, the optimized PW configuration can meet the irrigation needs of residents, indicating that the new method proposed in this paper has good potential for extension and application.