The Koktokay No. 3 granitic pegmatite, Altai, northwestern China, is a strongly zoned rare-element granitic pegmatite, where the petrographic zones were distinguished into two groups: outer zones (I to IV) and inner zones (V to IX). Nb-Ta oxides and zircon are investigated in this paper by using quantitative electron-microprobe analyses (EMPA) and backscattered-electron (BSE) imaging. Columbite-tantalite and zircon occur in most textural zones, whereas tapiolite and uranmicrolite are mainly restricted to zone VII. Manganocolumbite and zircon from the outer zones (zones II and IV) are homogeneous except for a few exceptions, whereas manganotantalite and hafnian zircon from the inner zones (V–VII) are obviously heterogeneous and strongly zoned. Chemically, Ta/(Nb+Ta) in columbite-tantalite and Hf/(Zr+Hf) in zircon increase from the outer to the inner zones on one hand, and from core to rim in single zoned crystals on the other hand. Observations of intra-zonal variations of the chemical composition of Nb-Ta oxides and zircon in the Koktokay No. 3 granitic pegmatite may suggest that the outer zones crystallize under magmatic conditions, whereas the inner zones crystallize under fluid-rich magmatic conditions, and locally under hydrothermal conditions. The extreme enrichments of columbite-tantalite in Ta, and of zircon in Hf, as well as the occurrence of uranmicrolite and tapiolite, indicate an elevated evolution of the Koktokay No. 3 granitic pegmatite.