Abstract: The Jizhong Depression hosts three prominent structural transfer zones—Hengshui—Wuji, Xushui—Wenan, and Baodi—Tongbaizhen—as well as the Niudong—Maxi strike-slip structural transfer zone, where carbonate geothermal resources with substantial yields and relatively high temperatures have been identified. To reveal the controlling mechanism of structural transfer zones on carbonate geothermal resources, newly acquired data, including water temperature, hydrochemistry, hydrodynamic fields, and ¹⁴C isotopic dating results of geothermal wells in typical structural transfer zones of the Jizhong Depression, are extensively compiled and supplemented in this study. Methods such as the Na-K-Mg equilibrium diagram, saturation indices of major minerals, and sodium-chloride coefficient were adopted to comprehensively characterize the thermal, hydrodynamic, and hydrochemical fields of carbonate geothermal water within and around representative structural transfer zones, and further analyze their indicative significance for structural belts and their tectonic activity features. Results indicate that structural transfer zones exert fundamental control on the sedimentation and evolution of adjacent strata, as well as the burial depth and hydraulic connectivity of carbonate geothermal reservoirs, thereby modulating the thermal, flow, and hydrochemical characteristics of groundwater in these systems to a significant degree. Specifically, the ascent of deep geothermal fluids along large strike-slip faults and deep circulation of groundwater along major deep faults elevate water temperatures in the vicinity of deep strike-slip fractures. For instance, geothermal wells at the intersection of the Niudong—Maxi and Xushui—Wenan structural transfer zones yield wellhead temperatures of 109.0–123.4 °C. Conversely, densely distributed tensional-normal faults within transfer zones act as dominant conduits, resulting in larger geothermal reservoir storage capacities but lower water temperatures. Structural transfer zones host abundant faults with variable fault properties, leading to complex controls on carbonate geothermal water. Extensional structural transfer zones are dominated by abundant groundwater, while strike-slip structural transfer zones readily provide conduits for deep heat sources. Future studies are recommended to conduct detailed fault structural analysis on structural transfer zones with densely distributed geothermal wells, so as to systematically clarify the constraint laws of fault structures on geothermal water.