China is located at the intersection of the Pacific Plate and the Mediterranean- Himalaya Tropics, where the Mesozoic and the Cenozoic sedimentary basins are well developed with abundant geothermal resources. In recent years, the development and utilization of geothermal resources in our country has been developing vigorously. However, in the absence of a comprehensive analysis of geothermal systems, there is a lack of geothermal exploration and development programs in different areas that are tailored to local conditions. This has resulted in confusion in the exploration and development of geothermal resources across the country. Based on the viewpoint of system theory, the genetic theory of “homologous symbiosis- crust- mantle heat generation- tectonic heat accumulation” is proposed in this paper. Furthermore, this paper takes the main hydro- geothermal systems in China as an example, establishes the viewpoint of System Theory of Hydrothermal System Analysis, and divides the main types of hydrothermal systems in China into seven types: Composite Hydrothermal system of Buried Hill type in the sedimentary basin, Layer- controlled Hydrothermal System in deep depression of the sedimentary basin, Geopressure- type hydrothermal system in the Fault basin, Plate- edge Hydrothermal System in the the Continental Collision Zone, Hydrothermal System of thermal control structure in the subduction zone of plate edge, Deep Circulation Type Hydrothermal System in the uplifted mountainous area and the Modern Volcanic Hydrothermal System. The movement conditions and heat source mechanism of these typical hydrothermal systems are analyzed, and the genetic models of different types of hydrothermal systems in China are summarized. This study presents the basic theory and method of geothermal resources research in our country, and provides the theoretical basis for regional geothermal resources exploration and development. It offers guidance for further scientific development and utilization of geothermal resources in China.