The Koktokay No. 3 pegmatite is the largest Li-Be-Nb-Ta-Cs pegmatitic rare-metal deposit of the Chinese Altai orogenic belt, and is famous for its concentric ring zonation pattern (nine internal zones) and rare-metal reserves. In this paper, we present the results of major and trace element analysis for garnet, tourmaline, and beryl from the outer to inner zones of the No. 3 pegmatite. From previous studies on tourmaline and beryl, potential tracers of the degree of pegmatite evolution could be found by comparing with accepted indicators and evolutionary trends from the outer to inner zones of this pegmatite. The Sc, Y, Li, Ta contents and Y/Ho value of garnet, together with the Ti, Ca, Na, Pb, Bi and REE contents of tourmaline, and the Fe, Ga and Rb concentrations of beryl could be possible tracers of the degree of evolution of pegmatites. The textures and internal structures (homogeneity, oscillatory pattern, heterogeneous rims, replacement structures) of minerals in the pegmatite suggest that the rock underwent (1) rapid undercooling and crystallization after emplacement, resulting in the formation of an unidirectional solidification texture (UST), and then (2) became relatively stable, forming coarse crystals in outer zones, and finally (3) experienced disequilibrium crystallization, leading to the formation of complex internal structures of minerals in the inner zones, mainly caused by exsolution of more fluid and the formation of immiscible melts with different alkali contents. The evolutionary trend and the internal structures of tourmaline and beryl indicate that the formation of the Koktokay No. 3 pegmatite was controlled mainly by fractional crystallization. The convex tetrad effect, non-CHARAC Y/HO values, and extreme Eu depletion of garnet suggest that immiscibility, which is a significant mechanism during the formation of the No. 3 pegmatite, occurred during emplacement. The differences in composition and internal structures of the minerals between the outer and inner zones of the No. 3 pegmatite suggest that there was an abrupt change, during transition from the melt stage to the melt–fluid stage, resulting from a decompression event, which led to the exsolution of the fluid and initiated the Li-Ta-Cs deposition in the pegmatite.