A large number of thermal springs are widely distributed along the deep suture zones and faults in the north section of the Sanjiang Orogenic belt in southeast Tibetan Plateau, connecting the two high-temperature hydrothermal areas in southern Tibet and western Sichuan. Whether the genesis of all geothermal water in the north section of the Sanjiang Orogenic belt is consistent is still an unanswered question. In order to fill the research gap of the high temperature geothermal system in this region, in this study, we classified the geothermal springs into three geothermal fields (Jinsha, Lancang, and Nujiang geothermal fields) and attempted to find clues by comparing the hydrochemical and isotopic characteristics of geothermal fluids in the three geothermal fields. The δ²H and δ¹⁸O composition of geothermal springs suggest that all thermal springs are replenished by the meteoric water. Low content of trace elements and low degree of oxygen isotope shift indicate that the partial melting of the crust at a depth of about 20 km mainly provide heat for all thermal springs in the geothermal fields through conduction. But due to the difference of tectonic conditions, there are two formation patterns of geothermal waters in the study area, one was controlled by regional faults, the other was controlled by the folded complex. The geothermal waters controlled by regional faults were heated after deep circulation, and the reservoir temperatures calculated by the Silica-enthalpy mixing model are 175–200 °C and 200–225 °C, respectively. But the geothermal waters controlled by the folded complex were heated after shallow circulation, and the reservoir temperature is only 100–125 °C. Upon rising to the surface, the geothermal waters mixed with cold groundwater to different degrees. The dissolution of Na/K-silicates and carbonate rocks controlled the formation of Na-HCO₃ and Ca·Mg-HCO₃ type water, respectively. But dissolution of halite and gypsum (or anhydrite) in some areas can lead to further diversity of hydrochemical species, resulting in the formation of Na-Cl, Na-HCO₃·Cl, Ca·Mg-SO₄ and Na-HCO₃.SO₄ type waters.