The Yadong area located in the central Himalaya is the intersection of the South Tibetan Detachment System and the N—S trending rifts. It is one of the key areas for studying the relationship between the north- south extension and the east- west extension in the Himalaya. The tectonic deformation and cooling processes in the Yadong area are of great significance to understand the uplift history and deep- shallow dynamic mechanisms of the Tibet Plateau. In this study, apatite and zircon (U- Th)/He low- temperature thermochronology and QTQt thermal history simulation were carried out along two sections of the Greater Himalayan Complex in the Yadong area of the southern Tibet to constrain cooling history since the Middle Miocene. Our data present apatite (U- Th)/He age ranges from 11.23 to 4.87 Ma among 10 samples in the GHC section. The ages of zircon and apatite (U- Th)/He in the Yadong- Gulu rift section range from 9.02 to 6.48 Ma and 8.63 to 6.13 Ma, respectively. Based on the comprehensive regional thermochronological data, it is suggested that the Greater Himalayan Complex in the Yadong area have experienced two stages of cooling and exhumation since the Miocene: the early rapid cooling phase in the Mid- Miocene (16~11 Ma) was controlled by the extensional detachment of the South Tibetan Detachment System (the Zherger La detachment fault). The difference of cooling rate before and after 11 Ma indicates that the driving force of denudation was changed. The structural transformation from north- south extension to east—west extension occurred at the Late Miocene (11 Ma). The second rapid cooling phase occurred in the Late Miocene to the Pliocene (10~5 Ma), which was induced by the extensional activity of the Yadong- Gulu rift. The extremely rapid cooling event with cooling rate (290 ℃/Ma) during 9~6 Ma revealed that the Yadong- Gulu rift initiated at 10 Ma. Along southward of the GHC section of the Yadong area, the apatite (U- Th)/He data generally show the “old- young- old” variation trend, implying that the Greater Himalayan Complex have experienced fast laterally extrusion event in the way of channel flow. Combined with previous published data of the Greater Himalayan Complex, we suggested that the cooling and exhumation process of the Greater Himalayan Complex is featured by remarkably spatial and temporal difference. Three cooling stages can be defined as 25~11 Ma, 10~5 Ma, and ＜3 Ma, corresponding to tectonic driven forces and dramatic climate changes.