Abstract As a robust accessory mineral in igneous rocks, the mineralogical and geochemical characteristics of zircon can record the lithological differentiation and magmatic–hydrothermal evolution of highly evolved granitic systems. The F-Rb–rich, highly evolved Baishitouquan pluton of NW China exhibits gradual lithological changes from leucogranite, amazonite-bearing granite, and amazonite granite in the lower levels of the pluton to topaz-bearing amazonite granite, topaz albite granite, and pegmatite in the upper levels. In this study, three types of zircon grains were identified in five lithological zones based on textural and chemical characteristics. Type I zircon, which mostly occurs in leucogranite and amazonite-bearing granite, exhibits oscillatory zoning in cathodoluminescence images and experienced low degrees of radiation damage (0.21–0.68 × 1015 α-decay events/mg), which is indicative of its magmatic origin. Type II zircon, which mostly occurs in amazonite granite and amazonite pegmatite, exhibits textures that are indicative of hydrothermal alteration (e.g., spongy texture, porosity, and microcracks), and has elevated concentrations of some cations, such as Ca and Al. Type II zircon contains a higher concentration of non-formula elements, including rare earth elements (REEs), and Hf, Th, and U, than Type I and III zircons. Additionally, Type II zircon exhibits a significant M-type lanthanide tetrad effect and experienced varying levels of radiation damage (3.75–11.72 × 1015 α-decay events/mg). These characteristics suggest that Type II zircon has a hydrothermally altered origin. Type III zircon, which is restricted to the topaz-albite granite, has the smallest crystal size among all types of zircon grains, shows a euhedral to anhedral mottled appearance, and is characterized by patchy, cloudy, or irregular zoning, with numerous fluid inclusions. This type of zircon contains higher concentrations of Ti (110–1030 μg/g) than other types of zircon grains. Additionally, this type of zircon experienced limited radiation damage (2.18–3.69 × 1015 α-decay events/mg), and has a smooth surface and homogeneous internal textures. These characteristics suggest that Type III zircon is the product of fluid interaction with hydrothermally altered Type II zircon. Accordingly, this type of zircon crystallized directly from a Zr-saturated hydrothermal fluid during the later stages of magmatic–hydrothermal evolution. These contrasting textural and compositional features of the three types of zircon grains are indicative of three stages of magmatic–hydrothermal evolution of the Baishitouquan pluton: magmatic, magmatic–hydrothermal transition, and hydrothermal. These magmatic and hydrothermal processes were involved in the enrichment, transport, and precipitation of rare metals, such as Rb. Accordingly, this contribution demonstrates that the textures and chemistry of zircon grains can serve as petrogenetic indicators for assessing magmatic–hydrothermal evolution and rare-metal mineralization in highly evolved granitic systems. Furthermore, this study presents a model of the magmatic–hydrothermal evolution of F-rich, highly evolved granitic systems through the lens of zircon.