Abstract: Different types of allanite occur in the Oytag granitic pluton of the West Kunlun orogenic belt, providing an ideal target for investigating the geochemical behavior of rare earth elements (REEs) during magmatic-hydrothermal processes. In this study, systematic petrographic and mineralogical investigations of allanite from the Oytag pluton were conducted through backscattered electron (BSE) imaging and in-situ electron probe microanalysis (EPMA). Based on BSE greyscale variations, spatial textural relationships, and mineral paragenesis, allanite can be subdivided into three stages. Stage 1 allanite is of magmatic origin, which appears as homogeneous bright grey domains in BSE images and occurs as euhedral prismatic crystals commonly enclosed within plagioclase or quartz, exhibiting a simple mineral assemblage. Stage 2 allanite is characterized by heterogeneous dark grey domains, irregularly distributed along fractures and grain margins of Stage 1 crystals, locally developing vermicular micro-textures and coexisting with metasomatic minerals such as epidote, fluorite, xenotime, and hellandite-(Y). Stage 3 allanite exhibits the lowest BSE greyscale, appearing as extremely dark, thin, and irregular reaction rims, and is associated with quartz, and albite. The major elements of allanite display a continuous evolution from Stage 1 to Stage 3. Stage 1 allanite is highly enriched in LREE (e.g., Ce), Fe, and Mg, with extremely low Ca and Al contents. In Stage 2 allanite, LREEs and Fe-Mg decrease significantly, accompanied by intense fluctuations in Si, whereas Ca and Al increase markedly, suggesting the influence of Ca-Al-rich deuteric fluids. Stage 3 allanite is characterized by the lowest LREEs, Fe, and Mg contents and highest Ca and Al contents, accompanied by stabilization of Si, indicating complete metasomatism by late-stage fluids. We propose that the Oytag pluton records a complete evolution from magmatic crystallization to multi-stage fluid alteration. (1) During the magmatic stage, primary allanite crystallized and became strongly enriched in LREE. (2) During the hydrothermal stage, Cl-rich but F-poor deep-seated magmatic hydrothermal fluids induced coupled dissolution–reprecipitation reactions of primary allanite, resulting in the outward loss of LREEs, whereas M-HREEs, due to their extremely low solubility in ligand-poor fluids, were precipitated in situ under local supersaturation to form hellandite-(Y) and xenotime. (3) The subsequent infiltration of back-arc basin seawater during Stage 3 led to the final open-system alteration of allanite. The continuous loss of LREEs during both hydrothermal processes differs from the formation process of regolith-hosted REE deposits in South China and reduces the metallogenic potential of this type of deposit in the West Kunlun region.