Petrography and geochemistry of the altered and unaltered host rocks surrounding the Koktokay No. 3 pegmatite revealed that the unaltered amphibolite is mainly composed of hornblende, plagioclase, and ilmenite. Beyond these primary components, the altered host rocks contain a few newly formed minerals, including biotite, tourmaline, chlorine, and muscovite. The alteration zone surrounding the Koktokay No. 3 pegmatite is limited to 2.0 m, characterized by biotitization, tourmalization, and chloritization. In the altered host rocks, the contents of SiO2, MgO, MnO, Na2O, and TiO2 did not vary greatly. However, Al2O3 showed a weak decreasing trend with the increasing distance from the pegmatite contact zone, while Fe2O3 and CaO showed an increasing trend. The contents of Li, Rb, and Cs in the altered host rocks were much higher than those in the unaltered host rocks, decreasing with distance from the contact. The chondrite-normalized rare earth element (REE) pattern of the altered and unaltered host rock was right-inclined from La to Lu, but enriched in light REEs over heavy REEs after hydrothermal alteration. An isocon plot shows that some oxides migrated in with an order of P2O5 > K2O > TiO2 > Al2O3 > SiO2 > MnO ≥ MgO, while others migrated out with an order of Na2O > CaO > Fe2O3. For REEs, the migration ratios are positive values with Cs > Rb > Li > Nb > Ta > Be, signifying that all REEs migrated from the exsolved magmatic fluid into the altered host rocks. It was concluded that diffusion was the only mechanism for migration of ore-forming elements in the alteration zone. The effective diffusion coefficients (Deff) of LiF, RbF, and CsF were estimated under a fluid temperature of 500–550 °C. Using a function of concentration (C(x,t)) and distance (x), the order of migration distance was determined to be LiF > CsF > RbF, with diffusion times of (3.39 ± 0.35) × 106, (3.19 ± 0.28) × 105 and (6.33 ± 0.05) × 105 years, respectively.