The Tethys Himalayan belt in the southern Qinghai–Tibet Plateau has been intruded by a large amount of leucogranite due to collisional orogeny. In addition, strong tectonic movements since the Cenozoic era have led to the formation of a series of dome structures accompanied by various types of mineralization. The Cuonadong Dome and Yalaxiangbo Dome, forming the “double dome” structure in the eastern part of the Tethys Himalayan Belt, are affected by different geological processes, resulting in differences in their deep structures and affecting the formation of polymetallic minerals. At present, geophysical research on the fine structure of the crust of the “double dome” structure is limited, making it difficult to fully understand the formation of different deep structures in the Tethys Himalayan dome belt. This hinders the progress of research on the genesis of dome structures and large-scale mineralization mechanisms in continental collisional environments. In this study, the ambient noise tomographic method was used to obtain the S-wave velocity structure of the upper crust of the Cuonadong Dome and the Yalaxiangbo Dome, and the following results were found: 1. there is a significant difference in the velocity structures of the two domes, with the core velocity structure of the Yalaxiangbo Dome showing an overall high velocity, extending downward for more than 9 km, while the core of the Cuonadong Dome exhibits low-velocity characteristics, with some high-velocity bodies occurring locally, which may be related to the later intrusion of leucogranite and extensional activity of the Cuona Rift. 2. There are significant differences in the S-wave velocities between the lead–zinc deposits and rare metal deposits in the study area; the lead–zinc deposits occur in basins and graben margins and have large variations in the S-wave velocity, which may be related to the involvement of basin brine in mineralization; below the tungsten–tin–beryllium deposits, the S-wave velocity exhibits high-velocity protrusions, with mineralization occurring at the front ends of the protrusions, which may be caused by crystallization differentiation of leucogranite. 3. The study area has abundant geothermal resources and obvious geothermal structural features. The low-velocity basin in the upper part of the upper crust is a heat storage layer, the low-velocity channel in the middle is a heat-conducting layer, and the lower part is a low-velocity heat source area that continuously supplies heat, forming a special geothermal structural model for the Cuonadong Dome and Yalaxiangbo Dome.