Dense distribution of granites and surrounding hot springs, the high anomalous heating rates of geothermal fluids and the high geothermal gradients in shallow crust in Southeast China are revealed by previous geothermal explorations. However, there have always been debates on the genesis of geothermal anomalies of Southeast China. It is imperative to look into the genesis mechanism of geothermal anomalies through selecting a typical geothermal field, and constructing fine crustal thermostructure. In this study, in-depth excavation is implemented for the previous data of geophysical exploration and deep drilling exploration in the Huangshadong area. We synthetically analyze the results of radioactive heat productions (RHPs), thermophysical properties of rocks and audio-frequency magnetotellurics (AMT) sounding. This study concludes that the coefficient of radioactive heat generation (RHG) of crustal rocks and conduction heat of concealed granites is the main formation mechanism of geothermal anomalies of South China, where occurs a Great Granite Province. There is a regional indicating implication for the genesis of geothermal anomalies, taking the Huangshadong geothermal field as a typical example. It is also an important reference to guide the exploration, evaluation, development and utilization of geothermal resources in this region.