The characteristics of Late Cenozoic tectonic uplift of the southern margin of the Qinghai-Tibet Plateau may be inferred from fluvio-lacustrine strata in the Zanda basin, Ngari, Tibet. Magnetostratigraphic study shows that the very thick fluvio-lacustrine strata in the basin are 5.89–0.78 Ma old and that their deposition persisted for 5.11 Ma, i.e. starting at the end of the Miocene and ending at the end of the early Pleistocene, with the Quaternary glacial stage starting in the area no later than 1.58 Ma. Analysis of the sedimentary environment indicates that the Zanda basin on the southern Qinghai-Tibet Plateau began uplift at ~5.89 Ma, later than the northern Qinghai-Tibet Plateau. Presence of gravel beds in the Guge and Qangzê Formations reflects that strong uplift took place at ~5.15 and ~2.71 Ma, with the uplift peaking at ~2.71 Ma.