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Graphical abstract Highlights • Y(OH) 3-n n+ ions are adsorbed on kaolinite mainly via Y atom and surface O atoms. • Ion hydrolysis and surface deprotonation affect the adsorption of Y(OH) 3-n n+ ions. • Adsorption energies increase with the increase of kaolinite deprotonation degree. • Adsorption energies decrease with the increase of the hydrolysis degree of Y3+ ion. Abstract The interaction of rare earth elements (REEs) ions with clay minerals is crucial for understanding the processing of mineralization, extraction and recovery of ion-adsorption rare earth. Theoretical studies based on density functional theory (DFT) were performed to investigate the adsorption of rare earth Y(OH) 3-n n+ (n = 1–3) ions on kaolinite surfaces of varying deprotonation degree depending on the solution pH. The Conductor-like Screening Model (COSMO) was used to simulate the water environment of adsorption. The calculated results showed that the surface electrostatic potential and frontier orbital are enhanced and increasingly localized around the exposed oxygen atoms with the increase of the deprotonation degree of kaolinite (0 0 1) surface hydroxyls. Y(OH) 3-n n+ ions are adsorbed mainly via the Y atom and the surface O atoms, and located over the center of Al-hexagonal ring on kaolinite (0 0 1) surface, and the center of Si-hexagonal ring on kaolinite (0 0 −1) surface. The adsorption energies increase with the increase of deprotonation degree of kaolinite (0 0 1) surface, and decrease with the increase of the hydrolysis degree of Y3+. The results of Mulliken bond length and population, atomic charge, electron density and density of states (DOS) revealed that Y(OH) 3-n n+ ions interact with kaolinite (0 0 1) surface through the combination of covalent and electrostatic bonding, while with (0 0 −1) surface mainly through electrostatic bonding. The above calculated results would provide some atomic-level insights for the interaction of rare earth ions with kaolintie surfaces in aqueous solution. [ABSTRACT FROM AUTHOR]