The Jizhong Depression is a typical Mesozoic and Cenozoic fault basin located in the northwestern part of the Bohai Bay Basin that has abundant hydrothermal and geothermal resources and enormous development potential. In this study, hydrochemical and isotopic analyses were conducted on water samples from the southern region of the Jizhong Depression. The formation and evolution processes of the deep geothermal water were analyzed, the circulation process of the deep geothermal water was determined, and the genetic mechanism of the geothermal systems was elucidated. The hydrochemical types of the geothermal fluids in the sandstone reservoirs in the research area are mainly Cl·HCO3−Na type, while the geothermal fluids in the carbonate reservoirs are mainly Cl-Na type and Cl·HCO3−Na type. The ion components in the geothermal water are mainly controlled by the dissolution of the carbonate rocks and the alternate adsorption of cations. The elevation of the geothermal water supply area is 763–1063 m, and the main source is precipitation from the mountainous areas in the western Taihang Mountains. The Na-K-Ca temperature scale and multi-mineral equilibrium method have relatively small errors and are suitable for the southern region of the Jizhong Depression, with average errors of 21.44 °C and 32.64 °C, respectively. The depth of the Jxw thermal storage cycle in the research area is 3033–5187 m, and the depth of the Ng thermal storage cycle is 1360–2862 m. The content of the main ions (Na+, K+, and Cl−) in the water samples of the study area is greater in the Jxw thermal storage than in the Ng thermal storage; the Jxw thermal storage water samples have lower γNa+/γCl− values than the Ng thermal storage; and the γSO42−/γCl− and γCl−/(γHCO3− + CO32−) values are greater than those of the Ng thermal storage, indicating that the Jxw thermal storage is located in a geological environment with better sealing, longer flow, slower water circulation, more complete leaching, and higher salinity than the Ng thermal storage. Part of the deep thermal storage is transmitted upwards through the rocks via thermal conduction, and part is transmitted upwards along fault channels via thermal convection, forming a convection–conduction-type geothermal system.