The Nb-Ta-bearing minerals are important rare-element minerals in granitic pegmatite and record the magma evolution process. The successive progresses on lithium deposit exploration have been achieved in the middle and eastern part of the Himalaya, China. This study focuses on the internal structures and chemical compositions of Nb-Ta-bearing minerals (columbite-group mineral and microlite) from the three spodumene-bearing pegmatite dykes and muscovite granite in Kuqu pluton. The columbite-group minerals (CGM) from the spodumene-bearing pegmatite dykes are columbite-(Mn) to tantalite-(Mn) with homogeneous, core-rim, patch, irregular, oscillatory and complex structures. There are three formation generations named as CGM-I, CGM-II and CGM-III. From CGM-I to CGM-II, columbite-Mn become more Ta- and Fe-rich and Y-poor formed from Ta- and Fe-rich fluxed melt or fluid after crystallization of Nb-, Mn-, and Y-bearing minerals. From CGM-II to CGM-III, there are no consistent evolution trends on Ta/(Nb+Ta) and Mn/(Fe+Mn) values, reflecting complex interaction between mineral and fluid. Microlite in spodumene-bearing pegmatite dykes and muscovite granite occur as homogeneous, core-rim and irregular-zoned crystals which reveal a Ta-Ca-rich fluid activity, boundary effect or Nb-rich fluid activity, and fluid disturbance under unstable crystallization environment. The TiO2, UO2, F contents and Ta/(Nb+Ta) value are possible indicators for magma evolution, but late fluid activity that could change the chemical compositions of microlite should be considered. The Nb-Ta-bearing mineral studies reveal the magma features and evolution process of the three spodumene-bearing pegmatite dykes in Kuqu pluton. The No.1 spodumene-bearing pegmatite magma is relatively rich in Fe and successively experienced crystallization of Fe-bearing minerals, Nb- and Mn-bearing minerals, and Ta- and Mn-bearing minerals with a late Ta- and Ca-rich fluid activity which is influenced by boundary effect. The No.2 spodumene-bearing pegmatite experienced crystallization of Nb- and Fe-bearing minerals followed by Mn- and Y-bearing mineral crystallization and buffer of Nb- and Ta-bearing mineral crystallization, and in the late stage of evolution, there is a Nb-rich hydrothermal metasomatism after a Ta- and Ca-rich fluid activity. The No.3 spodumene-bearing pegmatite magma is relatively enriched in fluxes and experienced Nb-, Mn-, and Y-bearing minerals crystallization coupled with complex interaction among mineral, melt and fluid, and a late Ta- and Ca-rich fluid activity. The Kuqu spodumene-bearing pegmatites experienced evolution from melt to rare-metal-rich and fluxed melt, and finally to complex fluids which include Ta-Ca-rich fluid and late Nb-rich fluid, etc. The occurrence, internal structure and chemical composition of Nb-Ta-bearing minerals reveal the evolution processes and late fluid activities of the granites and pegmatite dykes in the Kuqu intrusion.