The Lianyunshan Complex (LYSC) is a Nb-Ta-Li-Be rare metals mining area in northeastern Hunan, South China. The deposit is composed of a granite-type rare-metal pegmatite mineralization that occurs as dikes around the LYSC. The present study examines the genetic relationship, 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 the LYSC. Four minerals: columbite-tantalite (coltan), zircon, cassiterite, and monazite were investigated for their chemical and isotopic compositions. The coltan grains range from homogeneous crystals to zoned varieties with growth rims that result from equilibrium and disequilibrium reactions due to local changes in the physical and chemical conditions. These structures were altered by later metasomatic replacement processes related to the hydrothermal fluid activity and produced structures such as alteration rims, patches, irregular zonations, and complex zonations, with a corresponding increase in Ta. Coltan in OBP yielded two weighted mean 206Pb/238U ages of 135.9 ± 2.1 Ma and 120.5 ± 1.2 Ma, corresponding to magmatic (early-stage) and hydrothermal (late-stage) Nb-Ta mineralization ages, respectively. The cassiterite gives a weighted mean U-Pb mineralization age of 130.5 ± 3.9 Ma, which is interpreted as the magmatic-hydrothermal age (transitional stage). Zircon grains in OBP give a lower weighted mean U-Pb age of 121.5 ± 0.8 Ma, resulting from metamictization by the later fluid-assisted alteration and recrystallization in the late-stage hydrothermal event. Monazite grains from OFP yielded a weighted mean 206Pb/238U age of 137.1 ± 0.5 Ma, while zircon gives a mean U-Pb age of 130.3 ± 0.6 Ma. The ages of 137 and 130 Ma obtained for the OFP represent the magmatic (early-stage) and magmatic-hydrothermal stage (transitional) of OFP crystallization in the LYSC. Calculated zircon εHf (t) values and TDM2 ages from OFP (−7.6 to −5.4 and 1663−1532 Ma, respectively) and OBP (−8.7 to −8.2 and 1735−1704 Ma, respectively) are akin to those of the schist and metasandstone strata of the metasedimentary Lengjiaxi metasedimentary group—a melt source material to the LYSC composite batholith. We propose a long-lived ∼15 m.y. Nb-Ta-(Sn) mineralization model for the Lianyunshan complex.