The Qiangtang basin is located in the central Tibetan Plateau. This basin has an important structural position, and further study of its tectonic and thermal histories has great significance for understanding the evolution of the Tibetan Plateau and the hydrocarbon potential of marine carbonates in the basin. This study focuses on low temperature thermochronology and in particular conducted apatite fission track analysis. Under constraints provided by the geological background, the thermal history in different tectonic units is characterized by the degree of annealing of samples, and the timing of major (uplift-erosion related) cooling episodes is inferred. The cooling history in the Qiangtang basin can be divided into two distinct episodes. The first stage is mainly from the late Early Cretaceous to the Late Cretaceous (69.8 Ma to 108.7 Ma), while the second is mainly from the Middle-Late Eocene to the late Miocene (10.3 Ma to 44.4 Ma). The first cooling episode records the uplift of strata in the central Qiangtang basin caused by continued convergent extrusion after the Bangong-Nujiang ocean closed. The second episode can be further divided into three periods, which are respectively 10.3 Ma, 22.6–26.1 Ma and 30.8–44.4 Ma. The late Oligocene-early Miocene (22.6–26.1 Ma) is the main cooling period. The distribution and times of the earlier uplift-related cooling show that the effect of extrusion after the collision between Eurasian plate and India plate obviously influenced the Qiangtang basin at 44.4 Ma. The Qiangtang basin underwent compression and started to be uplifted from the middle-late Eocene to the early Oligocene (45.0–30.8 Ma). Subsequently, a large-scale and intensive uplift process occurred during the late Oligocene to early Miocene (26.1–22.6 Ma) and the basin continued to undergo compression and uplift up to the late Miocene (10.3 Ma). Thus, uplift-erosion in the Qiangtang basin was intensive from 44.5 Ma to about 10 Ma. The timing of cooling in the second episode shows that the uplift of the Qiangtang basin was caused by the strong compression after the collision of the Indian plate and Eurasian plate. On the whole, the new apatite fission-track data from the Qiangtang basin show that the Tibetan Plateau started to extrude and uplift during 45–30.8 Ma. The main period of uplift and formation of the Tibetan Plateau took place about 22.6–26.1 Ma, and uplift and extrusion continued until the late Miocene (10.3 Ma).