The enrichment of heavy rare earth elements (HREE) in the granitic host-rocks is crucial for generating ion-adsorption HREE deposits in South China. The Shitouping pluton, located in the southern part of Jiangxi Province, South China, develops large-scale HREE deposits in its weathering profile identified by recent geological surveys. These granites can be divided into medium to coarse-grained biotite monzogranite (MGBG), medium to coarse-grained syenogranite (MGSG) and fine-grained alkali feldspar granite (FGAG) based on field observations and mineral assemblages. New geochronologic results show that this composite pluton intruded during the Early Cretaceous (ca. 140 Ma). Three granitic units displaying comparable whole-rock Nd [εNd(t) = −4.5 to −3.4] and zircon Hf compositions [εHf(t) = −4.4 to +1.2], combined with mineral association, hydrothermally altered zircon and whole-rock geochemistry, indicate they were derived from partial melting of hybridized crustal source, followed by intense fractional crystallization and fluid metasomatism in the highly evolved granitic system. The MGSG and FGAG have higher Rb, Nb, HREE contents and Rb/Sr ratios, as well as lower Nb/Ta, K/Rb ratios in comparison with the MGBG, implying they are more evolved units. The overlapping magmatic zircon trace element compositions between MGBG and MGSG, coupled with the subvertical contact boundary between the FGAG and the MGBG, suggest that the generation of Shitouping pluton should be attributed to the periodic magma replenishment, remobilization, and differentiation process in the long-lived magmatic system rather than simple fractional crystallization from a single parental magma. Hydrothermally altered zircon with elevated concentration of HREE and the paragenetic relationship between LREE-phosphate and HREE minerals in the MGSG suggest that the fluid metasomatism promotes the migration and accumulation of HREE. This is consistent with the high HREE concentration recorded in the MGSG, which contains abundant HREE minerals associated with fluorites. Thus, this study highlights that magma differentiation and fluid metasomatism during the late magmatic stage could achieve the relatively high HREE contents in granites to favor the formation of ion-adsorption HREE deposits.