•Carbonate clumped isotopes validate the preservation of primary carbonate of the Gonjo Basin in the early and middle Eocene.•The Gonjo Basin was low (0.7 km) in the early Eocene and rose to 3.8 km in the middle Eocene.•Rapid uplift was induced by intracontinental subduction between the Lhasa and Qiangtang terrains. Views differ on the uplift history of the SE Tibetan Plateau and causal geodynamic mechanisms, yet reliable age-constrained paleoaltimetry in this region could test growth models of the entire plateau. Here we apply carbonate clumped isotope thermometry to well-dated carbonate paleosols and marls in the Gonjo Basin, SE Tibet, to reveal the topographic evolution of the basin. The sedimentary ages of carbonates of the lower and upper Ranmugou Formation are constrained to 54-50 Ma and 44-40 Ma, respectively. The temperature derived from carbonate clumped isotope thermometry indicates the mean annual air temperature (MAAT) of the Gonjo Basin in the early Eocene was ∼24°C, which is consistent with the warm climate indicated by palm fossils. The MAAT of the basin in the middle Eocene was ∼7°C, 17°C cooler than in the early Eocene. Carbonate clumped oxygen isotope thermometry-based paleoaltimetry shows the Gonjo Basin experienced a rapid uplift of 3.1 km, from ∼0.7 km in the early Eocene to ∼3.8 km in the middle Eocene. This rise explains the marked cooling. As a cause of this rapid rise, and the associated regional climate change transforming the landscape from desert to forest, we invoke crustal deformation and thickening induced by intracontinental subduction between the Lhasa and Qiangtang terranes that comprise the core of the Tibet.