Abstract: The Zibo Syncline Basin, a typical medium-deep hydrothermal karst geothermal reservoir in North China, is rich in geothermal resources. However, a long-standing lack of in-depth research on the heat source, water cycle processes, and formation mechanisms of the geothermal field has constrained its scientific exploration and development. Based on field investigations of geothermal wells, a total of 15 groups of karst thermal water and cold water samples were collected in the study area. Through analyses of major elements, hydrogen and oxygen isotopes, carbon isotopes, gas isotopes, and hydrochemical characteristics, the heat source, pathways, water source, and circulation mechanisms of the geothermal water were revealed. The results indicate five main points: (1) The average crust-mantle heat flow ratio in the Zibo Syncline Basin geothermal field is 1.35, indicating a predominantly crust-derived heat source. This mainly originates from heat accumulation controlled by the normal geothermal gradient during deep groundwater circulation. (2) The fault structural system controls the deep heat source and water source. (3) Hydrogen and oxygen isotope tracing indicates that the recharge elevation of the geothermal water ranges between 86.7 m and 381.4 m, and the recharge source is atmospheric precipitation. (4) The hydrochemical characteristics exhibit a distinct geochemical zonation along the recharge-runoff-discharge direction, revealing the following formation mechanism of the karst thermal water: after infiltration and recharge from atmospheric precipitation, the karst cold water evolves through deep circulation and confined stagnant flow under coupled structural-hydrological conditions. Based on this, a composite genesis model of “structural control–deep circulation–confined stagnant flow” is proposed. (5) The karst thermal water in this area has a strong recharge capacity, and under reinjection conditions, sustainable development is basically feasible. After atmospheric precipitation infiltrates in the southern limestone outcrop area, part of the groundwater enters deep circulation through the fault structural system, is gradually heated under the normal geothermal gradient, undergoes long-term confined stagnant evolution within the strata, and finally rises to the surface under structural control to form karst thermal water. This process is dominated by crustal-derived heat, with clear hydrochemical zonation, collectively forming a complete and sustainable water-heat circulation system.