The Koktokay No. 1 pegmatite in northwestern China is a highly fractionated Li-Cs-Ta (LCT)-type granitic pegmatite. As main Nb-Ta oxides in this pegmatite, columbite-group minerals (CGMs) not only display variations in Nb/Ta and Fe/Mn, but also are typified by noticeable Zr, Hf, and U contents. Here, we report on the chemical evolution and late-stage re-equilibration of CGMs in the processes of crystallization and evolution of this pegmatite. Columbite-group minerals record large variations in Ta/(Nb + Ta) values (0.06–0.98) and moderate variations in Mn/(Fe + Mn) values (0.58–0.99), which could be a result of fractional crystallization of pegmatite magma. The concentrations of ZrO2, HfO2, and UO2 in CGMs from the contact zone inwards to zone II of this pegmatite are uniformly less than 0.35 wt.%. However, primary tantalite-(Mn) with Ta/(Nb + Ta) and Mn/(Fe + Mn) values of 0.63–0.98 and 0.86–0.99, respectively, show relatively high contents of ZrO2, HfO2, and UO2, up to 1.68, 0.73, and 1.25 wt.%, respectively. The contents of ZrO2, HfO2, and UO2 are positively correlated with variations in Ta/(Nb + Ta) values within different grains and single grains of primary tantalite-(Mn). Crystal-chemical considerations suggest that Zr, Hf, and U are possibly present in the tantalite-(Mn) structure due to the substitution 3(Zr,Hf,U)4+ = 2(Nb,Ta)5+ + (Fe,Mn)2+. In some areas within the primary tantalite-(Mn) crystals in zone III, specific tantalite-(Mn) has been identified with sharp but irregular contacts with the host tantalite. Such tantalite-(Mn) is chemically depleted in Zr, Hf, and U, but contains many small inclusions of zircon, the MnZrTa2O8 phase, uraninite, and U-rich member of the microlite group of minerals. In a similar way, the primary Zr-Hf-U-bearing tantalite-(Mn) experienced late-stage local re-equilibration, giving rise to the formation of secondary Zr-Hf-U-depleted tantalite-(Mn) and other Zr- or U-rich mineral inclusions in an open fluid-mediated system. The behaviors of Zr, Hf, and U in CGMs in the Koktokay No. 1 pegmatite are indicative of Zr, Hf, and U enrichment during fractional crystallization of a highly fractionated pegmatite magma on one hand and imply late-stage activities of fluids on the other. Considerable enrichment of U and Hf in CGMs indicates that this type of mineral may act as a target for in situ LA-ICP-MS U-Pb dating and Lu-Hf isotope measurements, which may provide key information for understanding the source of the magma and the evolution mechanism of the Nb-Ta mineralization.