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Yttrium (Y) is a crucial rare earth element, and it is found in the ion-adsorption rare earth ore of Jiangxi province, China, at a percentage of up to 64.9%. This study used density functional theory calculations to investigate the adsorption behaviour and bonding mechanisms of the Y ion on the surface of kaolinite (001). Understanding these would be beneficial for its mineralisation processing and exploitation. [Y(OH) 2 (H 2 O) 7 + was studied as the initial adsorption structure with the lowest binding energy of −1629.19 kJ/mol in an aqueous system. The adsorption models were divided into outer-layer and inner-layer adsorption models based on the adsorption energy and bonding mechanisms. It was found that [Y(OH) 2 (H 2 O) 7 + preferred to adsorb on the Al-OH surface with inner-layer adsorption mainly via the coordination bond of Y–O s , and through hydrogen bonds for outer-layer adsorption. In the outer-layer adsorption, the adsorption energy of [Y(OH) 2 (H 2 O) 7 + on the Al-OH surface was higher than that on the Si–O surface because of the steric hindrance effect of the H in the hydroxyl of the Al-OH surface. The Mulliken bond populations of Y–O s for inner-layer adsorption showed that it was primarily dominated by the bonding orbital. [Display omitted] • The adsorption of hydrated Y3+ on kaolinite surface have been investigated with DFT. • Hydrated [Y(OH) 2 + tend to coordinate with more H 2 O ligands until 7 in aqueous. • The outer-layer adsorption of hydrated [Y(OH) 2 + were related to hydrogen bonds. • Hydrated [Y(OH) 2 + prefer to adsorb on Al-OH surface with inner-layer adsorption. [ABSTRACT FROM AUTHOR]