The late Cenozoic sediments in the rift basins in the northern Himalaya Mountains document important information about the uplift and deformation of the most active tectonic region in the Tibetan Plateau. However, these sediments have not been precisely dated, hindering our ability to address the basin development and termination associated with a series of uplifts in the southern Tibetan Plateau. Here, we report a detailed magnetostratigraphic study on the fluvio - lacustrine sedimentary sequence of the Dati Formation bearing abundant Hipparion forstenae fossils in the Dati Basin in the northern frontal region of the Himalaya Mountains. The 195 m – thick section yielded six normal and seven reversed polarity zones that correlate well with Chrons C3An.1r to C4r.2r of the geomagnetic polarity time scale, constraining the section age to ~8.6 – ~6.2 Ma. Together with the magnetostratigraphic results from other rift basins in the region, these results indicate that the horizons bearing the Hipparion fossils were deposited during the age interval of 7.1–6.5 Ma in the northern Himalaya Mountains. The regional tectonic activity and comprehensive magnetostratigraphic and sedimentologic comparisons suggest that the evolution of the rift basins in the northern Himalaya Mountains has involved three major stages since the late Cenozoic, i.e., (1) ~10.0–8.0 Ma, onset of the basins with fan delta facies; (2) ~8.0–3.0 Ma, expansion of the basins with mainly lacustrine facies; (3) ~3.0–1.7 Ma, shrinking and termination of the basins with alluvial fans. The basin evolutionary history indicates an accelerated tectonic uplift of the Himalaya Mountains at ~10.0 Ma, and two deformational events at ~3.0 Ma and at ~1.7 Ma.