The appearance of hydrous magmas and the following separation of volatile-rich fluids through hydrothermal alteration are intricately linked to the formation of granitic rare-metal deposits, the principal source of worldwide Li, Be, Nb, Ta and Cs production. The lack of mineralogical information from the developing magmatic–hydrothermal system has, however, prevented a thorough comprehension of these processes. Apatite occurs as an accessory mineral in the metasedimentary (schist)–magmatic (muscovite monzogranite)–pegmatite (ore-free or ore-bearing pegmatite) rocks in the Mufushan Complex (MFSC) rare-metal ore field of northeastern Hunan, South China, potentially providing insights into Nb–Ta–(Li–Be–Cs) mineralization. To demonstrate that apatite can potentially record the magmatic–hydrothermal evolution of metasedimentary–magmatic–pegmatite systems, this study presents a combined textural and geochemical study of apatite from the MFSC granitic pegmatite-type rare-metal mineralization. The MFSC apatite textures and compositions have changed since it first crystallized (i.e. post-crystallization alteration). Apatite from the schist shows a homogeneous rim or homogeneous textures with cracks or inclusions (S-ap1) and a patchy core (S-ap2), indicative of a magmatic–hydrothermal origin. Apatite from the muscovite monzogranite (G-ap) displays altered and distinctive core–rim textures, with visible voids, mineral inclusions and cracks, suggestive of overprinting of early magmatism texture by hydrothermal fluid. However, compared with S-ap1, S-ap2 and G-ap, the pegmatite apatite shows more complicated textures; that is, P-ap1 (homogeneous bright and dark areas) and P-ap2 (replacement texture involving alteration rim, growth zonation, patchy and complex zoning patterns). P-ap1 underwent early magmatism and weaker post-hydrothermal overprinting, and P-ap2 reflects a magmatic–hydrothermal product. S-ap1 and S-ap2 yield lower intercept ages of 130.6 ± 1.8 and 128.4 ± 3.8 Ma, respectively, which are consistent with the transitional age of the magmatic–hydrothermal metallogenic environment in northeastern Hunan. G-ap and P-ap1 yield older ages of 136.3 ± 2.8 and 141.3 ± 6.7 Ma, respectively, which correspond to the age of magmatic early stage (Nb–Ta)-mineralization within uncertainty in northeastern Hunan. The Sr isotopic composition of apatite provides evidence for the provenance of the MFSC batholith in the rare-metal metallogenesis of the Lengjiaxi Group. Therefore, we hypothesize that apatite in granitic rare-metal deposits within metasedimentary–magmatic–pegmatite systems might be employed as a viable proxy to explore the textures and geochemical fingerprints of fluid exsolution and hydrothermal alteration. Supplementary material: Analytical techniques and the results for apatite grains in this investigation are available at https://doi.org/10.6084/m9.figshare.c.7038699