Highly evolved granites can be important hosts of rare earth element (REE) resources, and more importantly, they commonly serve as the protolith for regolith-hosted REE deposits to form during weathering. Highly evolved granites in the Zudong pluton, South China, are extremely rich in the heavy (H)REE (up to 8000 ppm total HREE), and display significant REE fractionation. Moreover, the HREE enrichment is positively correlated with the degree of REE fractionation, indicating a unique process in preferentially enriching the HREE during the evolution of the granites. Multiple stages of hydrothermal re-mobilization of the REE can account for the HREE mineralization, and these are recorded in the texture and composition of the zircon. In these processes, fluctuations in the F activity of the fluid caused alternating dissolution-reprecipitation and continuous growth of the zircon. REE were repeatedly mobilized and enriched in the fluid to precipitate the major HREE mineral synchysite-(Y), and partially incorporated into the growth zone of zircon, while other elements were largely lost to the fluid during the extensive dissolution of the rock-forming minerals. LREE were also likely substantially mobilized in the late hydrothermal stage and lost through complexation with Cl, causing the significant LREE depletion and, thus REE fractionation. This process continuously enriched host granites in the HREE to a potentially economic grade, making them favorable protoliths for subsequent supergene regolith-hosted HREE deposits.