The regolith-hosted rare earth element (REE) deposits in South China are important sources of the world’s REE production. The alteration processes of primary REE-bearing minerals in granitic bedrock remain unclear so that the pathways of REE mobilization from primary minerals to regolith-hosted REE deposits have not yet been well established. Allanite is the principal REE repository in granitic bedrock and may have undergone alteration during deuteric fluid metasomatism and supergene weathering. Here, we document the allanite in the bedrock of the Zuokeng regolith-hosted REE deposit in South China to decode the REE mobilization during interaction of allanite with two different types of fluids. Most allanite grains have four distinct domains in the backscattered electron (BSE) images. Domain 1 is of magmatic origin and enriched in light REE (LREE), whereas Domains 2, 3 and 4 are of hydrothermal origin with different degrees of enrichment in middle to heavy REE (M-HREE). In particular, Domain 4 appears as overgrowth rims with the highest M-HREE concentrations among hydrothermal domains and likely crystallized from Cl-rich deuteric fluids exsolved from granitic magmas, evidenced by consistent U–Pb ages (ca. 159 Ma) and ε_Nd(t) values (-9.4 to -7.3) of Domains 4 and 1. The preferential removal of LREE and uptake of M-HREE from Domains 2 and 3 to Domain 4 is thus attributed to metasomatism by Cl-rich deuteric fluids. On the other hand, some allanite grains in weathered bedrock also interacted with F- and carbonate-rich groundwater and were gradually replaced by synchysite-(Ce) and calcite. Consequently, LREE were concentrated in synchysite-(Ce), whereas M-HREE may have been lost to groundwater. This study unravels that the enrichment of LREE and M-HREE in altered bedrock was initially facilitated by F-, carbonate-rich fluids and Cl-rich deuteric fluids, respectively, which are likely crucial for developing regolith-hosted LREE and M-HREE deposits in South China.