The weathering crust-type rare earth deposits occur widely in South China, but understanding of mechanisms of differentiation and enrichment of rare earth elements (REEs) during weathering process is still very limited. In this study, X-ray diffraction (XRD) and high-resolution transmission electron microscopy (HRTEM) methods were employed to better characterize the presence of REEs in the Zhaibbei rare earth deposit in southern Jiangxi Province. Our results showed that the Zhaibbei weathering profile of the rare earth deposit preserved the complete in-situ weathering soil layers, including saprolite layer, illuvial layer, eluvial layer, and topsoil layer from the bottom to the top. The saprolite layer contains mainly illite, smectite, and kaolinite. The illuvial layer and eluvial layer have similar clay mineral compositions of dominantly halloysite, kaolinite, and illite, with minor vermiculite, and the topsoil layer is consisted of mainly halloysite, with minor kaolinite and vermiculite. The heavy rare earth elements (HREEs) in the weathering profile are mainly associated with iron oxide minerals and are enriched in iron oxide minerals through substitution and co-precipitation, while the light rare earth elements (LREEs) are mainly associated with halloysite and kaolinite in ion adsorption. In addition, REEs in the upper profile can also form discrete secondary rare earth phosphate minerals. The enrichment and differentiation of REEs during the weathering process are mainly related to clay minerals and hematite. This study reveals occurrence of ore-forming REEs in the weathering crust-type rare earth deposit from the view of direct microscopic observation, which provides key evidence for the differentiation and enrichment process of REEs in rare earth deposits in the South China weathering crust.