Southeastern China (SE China) is located in the Pacific tectonic domain and has experienced a series of tectono-magmatic events induced by the subduction of the Paleo-Pacific Plate since the late Mesozoic. The subduction formed a series of NE-NNE oriented faults under a NW–SE regional stress field, along which a number of thermal springs occur. Previous studies have focused on the genesis mechanism of specific geothermal fields in SE China, but the general characteristics of hydrothermal systems in SE China remains unclear. In this study, we investigate the correlation between geothermal activity, hydrochemical type and regional faults by studying the distribution of hydrothermal activity and geochemical properties of typical hydrothermal systems in SE China. The hydrothermal systems in SE China have a crustal thermally-dominated structural origin unique to the specific geological and tectonic conditions of the Eurasian Plate margin. The upwelling of the asthenosphere and the widespread granitoids with high radiogenic heat production in SE China provide major heat sources for regional geothermal anomalies. The NE-oriented crustal thermally-dominated faults are critical for the formation of geothermal anomalies and NW-oriented extensional faults have created favorable conditions for meteoric water infiltration, transportation and the formation of thermal springs.