Regolith-hosted rare-earth element (REE) deposits are essential for supplying heavy-REEs (HREEs), meeting over 95% of global demand. In weathering crusts, REE enrichment and fractionation form these valuable deposits. While REEs are commonly thought to adsorb onto the Al-basal plane of kaolinite, the atomic-scale adsorption state has not been visualized, and the role of clay minerals in REE fractionation is debated. Using high-resolution atomic force microscopy (HR-AFM), we visualize the atomic-scale adsorption of light-REEs (LREEs) and HREEs on the Si-basal and Al-basal planes of kaolinite in aqueous solutions. Our results show that REEs primarily adsorb on the Si-basal plane, forming a "triangle" pattern, with HREEs preferentially adsorbed over LREEs, unequivocally establishing that clay minerals affect REE fractionation. This adsorption behavior is confirmed on mica, which also exposes Si-basal planes. This study reveals the unexpected significance of the Si-plane in REE adsorption, providing atomic-scale insights into REE enrichment and fractionation mechanisms during the metallogenetic process of regolith-hosted REE deposits. Moreover, the elucidated activity and specificity of the Si-basal plane indicate significant implications for various geochemical processes, such as elemental immobilization, transport, and cycling, due to the abundance of silicates within Earth’s crust.