Rare-metal granitic pegmatites are commonly considered to be the results of a combination of magmatic and hydrothermal processes. Although magmatic crystallization and fractionation, and magmatic-hydrothermal transition have been extensively investigated, the processes related economically valuable mineralization of rare-metals and strong fractionation of geochemical twins remain controversial. This study presents a comprehensive analysis of the geochemical evolution of rare-metal mineralized pegmatites, focusing on the mineral chemistry of muscovite and columbite-group minerals (CGM) from the Dangba rare-metal granitic pegmatites in the Songpan–Ganzê orogenic belt. Our findings suggest that the random orientation growth of spodumene crystals and widespread distribution of disordered columbite-group minerals crystals are indicative of lithium saturation in the initial melt at the Dangba No. VII dike. Magmatic fractionation is indicated by gradually increasing ratios of alkali metals (K/Rb ratios) and Ta# (Ta/(Ta + Nb)) in muscovite and CGM, and is proposed to be an important factor for enrichment of rare-metals. During the magmatic-hydrothermal transition, muscovite from metasomatism of spodumene exhibits similar or slightly higher levels of Li, Rb, and Cs, compared to primary muscovite, but shows strong depletion of Ta, Nb, Sn, and W. Alteration of primary minerals (e.g., spodumene, alkali feldspar, and columbite-group minerals) results in the release of these elements into the reactive media (melt/fluid) during the metasomatism. This process ultimately leads to the depletion of rare metals in the early crystallized minerals. However, this process is advantageous for the subsequent mineralization of Ta and Nb, as well as their fractionation. The chemical compositions of exsolved aqueous fluid are influenced by the mineralogy of pegmatites and the partitioning behavior between melt and fluid. Furthermore, pervasive albitization serves as an exploration criterion for Li–Ta–Nb in the Ke'eryin Orefield.