The tectonic affinity of the quartzite unit is essential for reconstructing the Cenozoic evolution of the Eastern Himalaya Syntaxis. We presented new petrographic and zircon U-Pb geochronological data from the quartzite unit collected from the western boundary of the Namche Barwa syntaxis. The maximum depositional ages indicated multiple depositional stages at >1800, 1122– 1136, 885, 451–493 and 54 Ma. Detrital zircon ages spanned from 50 to 3269 Ma with dominant populations at 500–900, 950–1400, 1550–1700 and 1750–2000 Ma. These age distributions suggested that the detritus were derived mainly from the Central Indian Tectonic Zone, Shillong Plateau and the Eastern Ghats Orogeny of the northeastern Indian subcontinent, and Western Australia. This provenance signature was distinct from the typical sequences of the Lesser Himalayan Sequence, Greater Himalayan Sequence and Tethyan Himalayan Sequence in the central–western Himalayas. Integrating our results with existing data from the Nyingchi Complex in the southern Lhasa terrane and Lesser Himalayan Sequence in the Eastern Himalayan Syntaxis, we proposed that the Namche Barwa syntaxis, Nyingchi Complex and Lesser Himalayan Sequence shared common source regions. Long-lived fluvial systems likely transported detrital material from northwestern Australia and the northeastern Indian subcontinent to these tectonic units.