Weathered granite of ion-adsorption rare earth elements (REEs) ore collected at Jiangxi Province, China was investigated to identify the minerals abundant in REEs. The analyses of scanning electron microscopy (SEM)-energy dispersive spectrometry (EDS) and laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) for individual mineral particles of the weathered granite showed that kaolinitic particles formed by K-feldspar weathering contained large amounts of REEs. Scanning transmission electron microscopy (STEM)-EDS analyses revealed that the kaolinitic particles were mainly composed of kaolinite, illite and hematite. The elemental maps by Nano-SIMS for the kaolinitic particle clarified that La and Y are particularly concentrated in illite. The presence of illite presumably contributes to the formation of the REE accumulation zone in weathered granite. Furthermore, in the in-situ desorption experiment, nearly half the REEs (45.5%) remained in the kaolinitic particle after the treatment with 0.5 M ammonium sulfate solution. The desorption ratio of heavy REEs (HREEs: Gd–Lu) (60.4%) was lower than that of light REEs (LREEs: La–Eu) apart from Ce (69.0%). These results suggest that REEs form inner-sphere complexes on the kaolinitic particle. It can be assumed that the inner-sphere complexation suppresses the extraction ratio of REEs from the ores by ion-exchange treatment.