Abstract: Deep geothermal water, a type of clean and low-carbon renewable energy, plays a significant role in achieving the goals of peak carbon dioxide emissions and carbon neutrality. However, its irrational exploitation will lead to many problems such as decreased water quantity, lowered water level, and low engineering benefits. Based on the available exploration data of geothermal wells in the urban area of Kaifeng City, Henan Province, this study constructed a hydrogeological model used to characterize the migration of geothermal water and a corresponding mathematical model, which was identified and verified using the Galerkin finite element method. Focusing on geothermal reservoirs at burial depths ranging from 1200 to 1400 m that are primarily exploited in the urban area of Kaifeng City, this study built an optimization model for the operation mode of production wells, aiming to overcome the drawbacks of isolated operation and on-demand exploitation of existing geothermal wells. In this model, the objective functions comprised the minimum drawdown, inter-well interference, and operating cost, and the constraint conditions included drawdown and the supply-demand balance. To improve the convergence accuracy and result reliability of the optimization model, this study solved the model using the Pareto-Grey Wolf Optimizer and ranked the results based on the TOPSIS theory. After optimization, the sum of drawdowns at partition nodes decreased by 70.3%, the sum of influenced drawdowns between geothermal wells decreased by 10.83%, and drawdowns in zones I, II, and III decreased by 12.85%, 28.14%, and 43.77%, respectively. The areas of the cones of depression surrounded by the -80 m and -90 m water-level contours decreased by 15.5% and 28.7%, respectively. Additionally, the total operating cost of geothermal wells decreased by 28.7%. By building an optimization model and introducing an improved algorithm, this study will provide a scientific basis for the rational exploitation of geothermal water. Optimizing the operation mode of geothermal wells can reduce the waste of water resources and improve their utilization efficiency while reducing the operating cost of geothermal wells. This study can serve as an important guide for the rational exploitation and scientific protection of geothermal water.