•Protoliths of Milin gneisses are ∼1556–1517 Ma continental arc-like granitoids.•Bulk-rock Nd and zircon Hf isotopes show their Paleoproterozoic material derivation.•The gneiss metamorphosed at ∼1200 Ma represents the Precambrian metamorphic basement.•Milin gneisses suggest the Lhasa terrane origins from the supercontinent Columbia. The Precambrian basement of the Lhasa terrane provides important information for understanding the formation and evolution of the Tibetan Plateau. However, due to the paucity of exposure, the properties of the Precambrian basement of the Lhasa terrane remain poorly known. Here we report zircon U–Pb ages, bulk-rock geochemical and zircon Hf isotopic data on the orthogneisses in the Milin area of the southeastern Lhasa terrane, southern Tibet. Inherited magmatic zircon cores of these gneisses yield protolith crystalline ages of 1556–1517 Ma, whereas the zircon rims give metamorphic ages of 1197–1192 Ma, both could be local provenance for the Mesoproterozoic detrital zircons in the Neoproterozoic–Paleozoic strata in the Lhasa terrane. Geochemical data indicate that the protoliths of the Mesoproterozoic rocks are continental arc-like granitoids with bulk-rock εNd(t) values of −3.7 to +0.7 (TDM2 = 1.99–2.34 Ga) and zircon core εHf(t) values of +1.8 to +8.6 (TDM2 = 1.71–2.17 Ga), suggesting their most likely derivation from partial melting of Paleoproterozoic crustal materials. We propose that the Mesoproterozoic gneisses in the Milin area represent the Precambrian metamorphic basement of the Lhasa terrane, likely related to the growth of Columbia supercontinent. Local exposure of the Precambrian metamorphic basement may be caused by crustal rapid uplift and erosion in the late Cenozoic and their inhomogeneous distribution.