Understanding the role of southeastern Tibetan thrust faults in the development of plateau topography is key to our assessment of the geodynamic processes shaping continental topography. Detailed structural analysis along the ~400 km long Jinhe-Qinghe thrust belt (JQTB) indicates post Late Eocene thrust motion with a minor left-lateral component, inducing ~0.6 to 3.6 km of apparent vertical offset across the fault. The exhumation history of the Baishagou granite, based on thermal modeling of new apatite (UTh)/He and fission-track results, suggests an accelerated exhumation rate (~0.4 km/Myr) between 20 and 16 Ma, corresponding to ~1.7–2.4 km of exhumation. We interpret this fast exhumation as a manifestation of the activation of the Nibi thrust, a northern branch of the JQTB, resulting in the creation of significant relief across the JQTB in the Early Miocene. When compared with previous studies, our findings show that Cenozoic exhumation and relief creation in southeastern Tibet cannot be explained by a single mechanism. Rather, at least three stages of relief creation should be invoked. The first phase is Eocene NE-SW compression partly coeval with Eocene sedimentation. During the Late Oligocene to Early Miocene and coeval with the extrusion of Indochina, the second thrusting phase occurred along the Yulong and Longmenshan thrust belts, and then migrated to the JQTB at 20–16 Ma. The third phase involved the activation of the Xianshuihe fault and the re-activation of the Longmenshan thrust belt and the Muli thrust. Uplift in the hanging wall of thrust belts appears to explain most of the present-day relief in the southeastern Tibetan Plateau.