Numerous Neoproterozoic magmatic and metamorphic events in the Altun–Qilian–North Qaidam (AQNQ) region record Grenvillian orogenesis and amalgamation of the supercontinent Rodinia. However, the tectonothermal regimes responsible for these Neoproterozoic events and the assumed position of the AQNQ in Rodinia remain controversial. Zircon U–Pb age data show that the orthogneiss and paragneiss/schist of the AQNQ experienced concurrent magmatism and metamorphism at 895–925Ma. Zircon Lu–Hf isotopic data indicate that the gneisses in the AQNQ have εHf (0.9Ga) values and tDM2 (Hf) model ages ranging from −5.6 to +3.9 and 1.4 to 1.9Ga. These data suggest that the early Neoproterozoic magma in the AQNQ was predominately derived from a late Paleoproterozoic–early Mesoproterozoic crustal source between 1.4 and 1.9Ga, marking an important episode of crustal growth in the AQNQ. The Neoproterozoic magmatism is geochemically characterized by (1) high SiO2, K2O, and low P2O5; (2) A/CNK ratios >1.0, ranging from 1.03 to 1.09; (3) enrichment in Rb, Th and U, and depletion in Ba, Nb, Ta, Sr, Ti, and Eu. Based on the geochemical resemblance to high-K calc-alkaline I-type granite and zircon Lu–Hf isotope signatures, the Neoproterozoic magmatism in the AQNQ was probably derived from ancient mafic-intermediate igneous rocks in an active continental margin. The Neoproterozoic tectono-magmatic–metamorphic history of the AQNQ, directly associated with the South China block (SCB) and the Tarim block (TB), indicates that the AQNQ and the TB coexisted as a single block in the early Neoproterozoic, which was temporarily connected to the SCB to the north or west in Rodinia during the late stages of the Grenvillian orogeny (950–900Ma).