Abstract: The Jinan karst aquifer system contains abundant cold groundwater and geothermal resources. However, these two resource types have long been assessed separately, and a unified water-balance analysis framework at the catchment scale has been lacking, thereby impeding the coordinated and sustainable development of both groundwater and geothermal resources. To address this critical issue, a three-dimensional coupled numerical model of the complete karst aquifer system is developed at the catchment scale, encompassing five karst water subsystems (Dongping Lake, Pingyin–Dong’e, Changxiao, Baotu Spring Catchment, and Baiquan Spring Catchment) together with the Jibei geothermal field. The model is used to quantitatively evaluate the sustainable co-exploitation yields of groundwater and geothermal resources under the constraint of maintaining perennial spring outflow, and to reveal the mutual constraints and co-exploitation thresholds between upstream cold groundwater abstraction and downstream geothermal extraction. The model is constructed using the COMSOL Multiphysics platform, integrating regional hydrogeological borehole data, long-term groundwater-level monitoring records, and field measurements of geothermal well production and reinjection. Through parameter inversion, dynamic water-level calibration, and water-balance computations, a first quantitative assessment is provided of the sustainable exploitation capacity and co-exploitation potential of the coupled system. The results indicate that, under current exploitation conditions, the subsystems of the Jinan karst aquifer are hydraulically connected to varying degrees through fault zones and karst conduits, and the entire system maintains a dynamic equilibrium between recharge and discharge. In the middle and upper reaches of the catchment, which serve as the direct recharge and runoff zone for the spring system, the sustainable groundwater exploitation yield is 473500 m³/d while simultaneously ensuring sustained spring outflow and water-supply abstraction. In the lower reaches of the catchment (Jibei geothermal field), by adopting a balanced production–reinjection development mode and optimizing the wellfield layout and extraction–reinjection rates through numerical simulation, the sustainable geothermal water exploitation yield is 43300 m³/d without inducing thermal breakthrough or affecting upstream spring outflow. After 50 years of equivalent reinjection under unpressurized conditions, the drawdown at each production well meets the regulatory requirements. These findings provide a scientific basis for the synergistic and sustainable development of groundwater and geothermal resources in the Jinan karst aquifer system under the constraint of sustained spring outflow, and offer a pathway for resolving the conflicts among spring protection, water supply, and heating demand.