As one of the most important accommodation zones during the India-Asia collision, the southeast margin of the Tibetan Plateau (SEMTP) is characterized by many large-scale strike-slip faults, a regional low-relief relict that has been deeply incised by several continental scale rivers that originate from central Tibet, and numerous plant and vertebrate fossil biotas residing in Cenozoic sedimentary basins. Therefore, the SEMTP not only provides a meaningful constraint on the geodynamic evolution of the Tibetan Plateau, but also serves as an exemplar to understand the various interactions among surface uplift, drainage network reorganization, climate change, and biodiversity. Precise dating of Cenozoic sediments in the basins of the SEMTP is crucial for understanding these processes. Previously, the geochronologic framework of Cenozoic sediments in the SEMTP largely relied on fossils and regional stratigraphic correlations, which often involved circular reasoning and large uncertainties. In the past two decades, high-resolution magnetostratigraphy, detrital zircon geochronology, and isotopic dating of interbedded tephra layers have been carried out on SEMTP Cenozoic sedimentary basins in Yunnan and eastern Xizang provinces, SW China. Using these new data, we build a revised chronostratigraphic framework for Cenozoic sediments in SEMTP, and use this updated temporal framework to contextualize regional tectonics and climate change. The new chronostratigraphic framework shows that (1) many of the “Neogene” sedimentary basins based on plant fossils and regional lithostratigraphic correlation in the SEMTP were actually formed in the late Eocene and early Oligocene; (2) most of the Paleogene sedimentary successions in the SEMTP ended at the late Eocene-early Oligocene and were unconformably overlaid by Middle-Late Miocene sediments. Oligocene-Early Miocene sediments are often regionally absent. Sedimentary structures within the basin successions show that Paleogene basins were generally formed in compressional settings while the Late Miocene basins were mostly developed in extensional settings. The new chronostratigraphic framework, together with analyses of sedimentary basin structures, suggests that the SEMTP began to experience crustal shortening early in the India-Asia collision (∼50 Ma), producing Paleogene sedimentary basins and giving rise to the subsequent widespread surface uplift and regional erosion in the Oligocene-Middle Miocene. Tectonic inversion from compression to extension since the Middle Miocene precludes significant uplift of the SEMTP after this time, which may be related to geodynamic changes in the evolution of the Tibetan Plateau.