Abstract: Fujian Province is one of the most important geothermal anomaly areas that located in the southern margin of China. It is of great significance for the scientific utilization of geothermal resources to reveal the formation mechanisms of geothermal system in the area. The circulation and evolutionary characteristics of geothermal fluid was clarified, correspondingly the conceptual formation mode and driving force of hydrothermal system established in each hydrogeochemical zone based on the implication of hydrochemical and isotopic characteristics of geothermal water samples, GIS spatial analysis, and the overview of regional geothermal geological and crustal thermal structure conditions. The results show that the geothermal system in Fujian Province can be divided into deep circulation convection type of uplifted mountain faults in northwestern region, complex convection conduction hydrothermal type of fault basin in southeastern region, and deep circulation convection type of fault depression zone in eastern and southeastern region. The endowment of geothermal resources in Fujian is controlled by regional tectonics and crustal thermal structure that the geothermal systems of Wuyi uplift zone in western Zhenghe-Dapu fault and the coastal margin zone in eastern Fujian obtained different crust and mantle heat source composition, but relatively uniform hydrothermal transmission channels. The heat accumulation of the geothermal system in the Wuyi uplift zone is mainly derived by mantle conduction, while the lithospheric thermal structure of eastern volcanic depression zone is the “hot crust-cold mantle" type that radioactive element decay of intrusive-volcanic rock mass contributed a relatively high amount of crustal heat accumulation. The regional tensile torsional NW faults were turned out to be the water conducting channels of geothermal systems, while pressure dominated NE faults be the water-blocking and heat-conducting channels for heat acumination. The standard head of total geothermal driving force generated by temperature rise and salinity increase in hydrothermal system of northwestern, southwestern, eastern volcanic depression zone and coastal margin region was ＋218.75 m, ＋202.24~＋250.60 m,＋261.72 m and ＋308.32 m respectively. The Yongmei depression zone in western Fujian, besides intersection zones of regional NW and NE deep faults, namely the hydraulic fracture of the faulted basin and the sunken bay extends deep into the mainland, the basement uplift zone of fault basins such as Fuzhou and Zhangzhou basin, intersection zones of regional NE deep faults and ring-shaped volcanic apparatus in eastern Fujian were the optimal target areas for exploitation of medium-high temperature geothermal resource in the bulk horizons.