The East-Qinling pegmatite district located in the North Qinling terrane is the largest one in the Qinling orogen, Central China. It is famous for its rare-element (REL) reserves, but its genesis is unraveled. We present in-situ major- and trace-element chemistry and U-Pb dating analysis of columbite-group minerals (CGM) and wodginite from representative Li-, Be-mineralized and barren pegmatite dykes. The mineralogical researches reveal that Li-mineralized pegmatite formed from a highly-evolved fluxes-rich magma, experiencing a magmatic stage at undercooling condition and a post-magmatic stage involving disturbance by alkali liquid or hydrothermal fluid. The lithium mineralization is accomplished by fractional crystallization after emplacement, alkali-fluid replacement or overprint of two Li-rich magmas. CGM Fe-Mn fractionation and REE distribution patterns with tetrad effect are considered as indicators to identify generations of CGM and trace the evolution of pegmatite formation. The CGM and zircon U-Pb ages suggest that the REL pegmatites formed in 422-410 Ma (Period I) and 399-384 Ma (Period II) and an early pegmatite magma activity occurred in 447-443 Ma. The late Ordovician-early Silurian and Period II pegmatite magmas stem from partial melting of North Qinling unit in collision and post-orogenic extensional settings, respectively, whilst Period I pegmatites formed in a weakening convergence setting by anatexis of fertile metasedimentary rocks or extremely fractional crystallization of granitic magma. The early-Paleozoic evolution of the North Qinling terrane contribute to the formation of large-scale East-Qinling REL pegmatites on the aspects of magma production and subsequent emplacement by crustal thickening, crustal reworking and dynamic extension during crust uplift.