The volcanic‐hosted Xiangshan uranium ore field is the largest uranium deposit in Jiangxi Province, South China. In this ore field, Pb–Zn mineralization has been discovered beneath the uranium orebodies at Niutoushan‐Heyuanbei area. Apatite is a ubiquitous accessory mineral in the volcanic rocks, as well as the U and Pb–Zn alteration–mineralization zones. Six main types of apatite, which show the evolution of volcanic magma and hydrothermal fluids, have been observed on the basis of textures, associated mineral assemblages, chemical compositions (halogen, MnO, FeO, and SO3, etc.), and mineral inclusions. For magmatic primary apatite, porphyritic lava‐hosted P‐Apa and P‐Apb have higher F/Cl ratios and lower contents of MnO and FeO than rhyodacite‐hosted R‐Ap. For hydrothermal apatite, U‐Ap1‐a, U‐Ap1‐b, and S‐Ap1 are recognized as hydrothermal‐affected apatite, while U‐Ap2 and S‐Ap2 as apatite precipitating from hydrothermal fluid. U‐Ap1‐a and U‐Ap1‐b, hosted in the green‐stained alteration zone, are characterized by highly heterogeneous BSE imaging and contain monazite and ThSiO4 inclusions. Such apatites record the remobilization and reprecipitation of rare earth elements (REEs), Th and U by a relatively high‐temperature, F‐ and CO2‐enriched but Na‐depleted fluid at the early REE‐phase stage. U‐Ap2 occurring in pitchblende–fluorite dominated ore sample, is featured with negligible Cl, variable F and relatively higher Ti contents. It records a new hydrothermal pulse of relatively low temperature, oxidized, highly Ca‐, Ti‐, and F‐enriched but Cl‐depleted which probably conduces to leaching and transporting significant amounts of uranium. S‐Ap1 and S‐Ap2 hosted within the sericite–quartz–carbonate alteration halo on both sides of Pb–Zn–Fe sulphide veinlets, have relatively high Cl and variable F content. This apatite records reduced, Cl‐, Ca‐enriched, magmatic‐derived fluid events. Combined with previous researches, the apatite data suggest that U and Pb–Zn mineralization may form from two spatially and temporally distinct hydrothermal systems. Thus, apatite can fingerprint multi‐stage hydrothermal fluids and be treated as a useful tool for mineral exploration.