The Xining Basin lies in the transitional zone between the arid Asian interior and the East Asian monsoon region. The continuous Cenozoic sediments in the basin provide a unique archive recording the uplift of the Tibetan Plateau and its environmental effects on central Asian aridification and Asian monsoon evolution. However, sediments deposited since the middle Middle Miocene have not been precisely dated, hindering our ability to address these issues. Here we dated a 336 m‐thick section containing many Late Miocene fossil mammals from the eastern basin. High‐resolution paleomagnetism revealed 16 normal and 16 reversed zones that correlate well with chrons 3n to 5Ar.1r of the Geomagnetic Polarity Time Scale, constraining the section to ∼12.7–4.8 Ma. The changes in lithofacies from floodplain to braided river at ∼8.6 Ma and to thick alluvial fan at ∼6.3 Ma with predominantly southerly paleocurrent directions occur simultaneously with an increase in the sedimentation rates, representing two periods of rapid uplift in the eastern Qilian Shan to the north. Our results provide a robust oldest age constraint (<4.8 Ma) on the ancient Huang Shui and Yellow River terraces on the basin sediments and eolian deposits on the terraces. The presence of well‐developed floodplain paleosols, shallow lake marls, and many large mammals in the lower section suggests that the monsoon climate in the late Middle Miocene to Late Miocene was more humid and stronger than that at present.