This paper is the result of hydrogeological survey engineering. Objective Meteoric water in the mountain areas infiltrates deep underground and circulates to the surface. It involves deep structural and hydrogeochemical processes, and it is one of the fluid source of forming rich geothermal and mineral resources. Predecessors focused on the groundwater source, circulation depth and flow system using methods of hydrochemistry isotope and numerical simulation, and further evaluated the distribution of regional geothermal and mineral resources. Methods Based on the data of DEM, fault structure, and lithology of the Yangbajing–Ningzhong basin,we establish 3D geometry finite element model. The standard saturated groundwater flow equation is solved using groundwater simulation software, and we analyse the circulation system of the typical hot springsand regional groundwater migration. Results The simulation results show that the maximum circulation depths of groundwater are respectively 5–7 km, 3.5–4 km, and 3–3.6 km at Yangbajing, Laduogang, and Qucai springs, and the corresponding groundwater circulation times are 23–80, 5–6 and 4–8 years. The groundwater of Nyainqentanglha Mountain seeps down to 10 km depth, where the time spans million years. Conclusions In general, the circulation depth and the recharge time of hot springs are different due to their different supply sources and circulation paths. Notably, there is no hydraulic connection between the hot springs at Yangbajing, Laduogang, and Qucai, although they are located in the same rift valley. It results in differences in material composition among these springs.