The initial timing of uplift on the southeastern side of the Longmenshan-Yalong-Yulong thrust fault zone remain under debate, with estimates ranging from the mid- to late Miocene, to late Eocene-early Miocene, which requires us to explore the history of its regional exhumation. Therefore, we analyzed the AFT age of Jiaozi Shan region in Central Yunnan Block, combined with the method of thermal history inversion. Results displayed that the Jiaozi Shan region experienced two rapid uplifting events at 40–26 Ma and 9–3 Ma respectively. River longitudinal profiles can record the history of regional tectonic uplift. We extracted the longitudinal profiles of the Pudu River and its 18 tributaries, meanwhile analyzed their geomorphologic parameters, including the slope, knickpoint elevation, and normalized channel steepness index (
ksn). The results show that there are generally two stages of knickpoints in the Pudu River Basin, which is in agreement with the two periods of exhumation revealed through thermal history inversion. Geomorphic parameters of the upstream and midstream segments of the tributaries display a systematic trends. The observed linear variations of geomorphic parameters indicate that, apart from the surface uplift caused by tectonic extrusion, at least 26 Ma, the regional uplift of the southeastern Tibetan Plateau driven by lower crustal flow is also a pivotal factor. In the downstream segment, geomorphic parameter also exhibit more pronounced systematic variations, likely due to to the mass flow of the lower crust towards the interior of the block, which commenced in the late Miocene.