The Cuonadong Sn–W–Be polymetallic ore deposit is the first rare-metal deposit related to leucogranites with giant mineralization potential to be discovered in the Himalayan Orogen. However, the post-mineralization exhumation and preservation processes of this deposit have not yet been studied in detail, although these factors are key to the exploration and evaluation of rare-metal deposits in the Himalaya. Geophysical data have revealed that a hidden fault (i.e., the Jisong secondary fault) cuts the southern part of the Cuonadong ore deposit. In order to determine the effects of the Jisong secondary fault on the exhumation of the Cuonadong deposit, we undertook zircon and apatite (U–Th)/He dating, apatite fission-track dating, and forward and inverse thermal history modeling of the footwall and hanging wall of the Jisong secondary fault. Our results show that the Cuonadong deposit experienced two stages of rapid, post-mineralization exhumation at ca. 10–9 and ca. 5–4 Ma, separated by a period of differential exhumation at ca. 9–5 Ma. These exhumation events were likely caused successively by the arc-shaped Nading Fault, normal faulting on the Jisong secondary fault, and thrusting on the Main Himalayan Thrust, although climate-related erosion may have also had a role in the exhumation. Owing to normal displacement on the Jisong secondary fault, the Cuonadong ore deposit underwent differential exhumation of 300–700 m. This implies that the eastern part of the deposit is more favorable for exploration than its western part if the deposit has the same mineralization depth. This study demonstrates that low-temperature thermochronological methods can be useful in the exploration for rare-metal deposits in the Himalayan Orogen.