The Mufushan Complex (MFSC), located in northeastern Hunan, is a significant producer of Nb-Ta-Li-Be rare metals in South China. The present study examines the genetic relationship, material provenance, fluid evolution, and metallogeny of the co-developed ore-free pegmatite (OFP) and ore-bearing pegmatite (OBP) in granite-related pegmatite-type Nb-Ta rare-metal deposits in MFSC. Three minerals (columbite-tantalite (coltan), zircon, and monazite) were chosen for analysis. The coltan grains display both primary crystallization structures (crystal homogeneity, oscillatory zonings, and primary growth rims) resulting from equilibrium and disequilibrium reactions due to localized changes in the physicochemical conditions and environment, as well as later replacement structures (alteration rims, patches, irregular zonations, and complex zonations) from metasomatic replacement processes related to hydrothermal fluid activity. The coltan yielded two weighted mean 206Pb/238U ages of 138.1 ± 2.1 Ma and 125.3 ± 2.0 Ma corresponding to magmatic and hydrothermal Nb-Ta mineralization ages. For the OFP, zircons also yielded two weighted mean 206Pb/238U ages of 138.4 ± 0.8 Ma and 131.5 ± 0.7 Ma, whereas monazite gave a weighted mean U-Pb age 142.9 ± 1.2 Ma. The ages of 142–138 Ma and 131 Ma represent the early and late stages of OFP crystallization and barren pegmatites in the MFSC, respectively. Zircon Lu-Hf isotopic compositions link rare-metal metallogenesis to the Lengjiaxi Group, which was the source material to the Mufushan composite batholith. Calculated εHf(t) values and TDM2 ages from the OFP (−7.6 to −3.6 and 1676–1418 Ma, respectively) and the OBP (−14.1 to +4.9 and 2976–1548 Ma, respectively) are akin to those of schists and metasandstones of the metasedimentary Lengjiaxi Group. We propose a long-lived (ca. 13-Myr) event involving two metallogenic episodes of Nb-Ta mineralization in the Mufushan region. This study demonstrates the potential of zircon, coltan, and monazite for fingerprinting minerals and classifying the mineralization potential of pegmatite veins.