The Jiajika deposit in western Sichuan is the largest pegmatite-type lithium deposit in China, but the mechanism of rare metal element enrichment in this giant deposit remains a topic of debate. This study presents a comprehensive Fe isotope study of granites, aplites, pegmatites, metamorphic rocks, and associated mineral separates from the 3211 m long deep Jiajika scientific drilling core (JSD-1) to constrain the magmatic-hydrothermal processes in the Jiajika deposit. Aplites and pegmatites have variable δ56Fe values that range from –0.12 ± 0.02 ‰ to 0.38 ± 0.02 ‰, by contrast, two-mica granite samples show limited variation in δ56Fe compositions (0.11 ± 0.04 ‰ to 0.21 ± 0.04 ‰). The Fe isotope data of the coexisting Fe-bearing minerals can impose critical constraints on crystal fractionation. Garnet shows the lightest δ56Fe compositions (–0.19 ± 0.06 ‰ to –0.06 ± 0.02 ‰) and tourmaline has the highest δ56Fe values (0.15 ± 0.01 ‰ to 0.22 ± 0.02 ‰) among all the investigated minerals, whereas the δ56Fe values of biotite range from 0.06 ± 0.02 ‰ to 0.18 ± 0.02 ‰. According to the compositional homogeneity of minerals and the relatively consistent offsets in δ56Fe between the three Fe-bearing mineral pairs, the co-existing Fe-bearing minerals in the Jiajika granitic pegmatites are interpreted to be in Fe isotope equilibrium. Additionally, based on the differences in mineral composition and geochemistry of bulk-rock samples at different observation depths, as well as the modeling results, the significant Fe isotope variation in Jiajika deposit reflect the combined results of biotite fractionation, hydrothermal alteration (tourmalinization), and garnet accumulation during multistage magmatic-hydrothermal processes. Spodumene-bearing pegmatites located in the upper portion of the drill core exhibit enrichment in heavy Fe isotopes (0.18 ± 0.04 ‰ and 0.30 ± 0.03 ‰) which can be attributed to their higher degree of magma evolution and the most abundant magmatic fluids related to enrichment and migration of rare metals. Furthermore, we conducted a comprehensive statistical analysis on the available Fe isotope data of granitic pegmatites, providing new insights into granite-pegmatite systems and related rare-metal mineralization processes from a Fe isotope perspective.