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Montmorillonite is a major mineral present in ion-adsorption rare earth ores, and the microscopic adsorption states of rare earth ions on its surface are of a great significance for the efficient exploitation of ion-adsorption rare earth ores. In this article, density functional theory calculations were used to investigate the adsorption mechanisms and bonding characteristics of hydrated Pr, Mg and NH₄ ions on the (001) surface of montmorillonite. Pr³⁺ exhibited a directed tendency geometry with Pr(H₂O)₁₀³⁺, which was adsorbed onto montmorillonite by hydrogen bonding with an adsorption energy of −1182 kJ/mol, and one coordinated H₂O ligand was separated from the first hydration layer of Pr. Both hydrated Mg and NH₄ ions were adsorbed onto the montmorillonite surface through hydrogen bonds, and the adsorption energies were −206 and −188 kJ/mol, respectively, indicating that the adsorption stability of the hydrated Mg ion was slightly higher than that of the hydrated NH₄ ion, but both were lower than that of hydrated Pr (−1182 kJ/mol). Hence, higher concentrations of Mg and NH₄ ions than rare earth ions would be necessary in the leaching process of ion-adsorption rare earth ores. Additionally, desorption experiments revealed that the recovery of Pr³⁺ by Mg²⁺ with a concentration of 38 mmol/L is 80%, while it is only 65% with the same concentration of NH₄⁺, and the concentrations of Mg²⁺ and NH₄⁺ were much higher than that of Pr³⁺ in lixivium, which is consistent with the DFT calculations.