Abstract: In the process of leaching of ionic rare earth ore, the leaching agent ammonium ions exchange the rare earth ions adsorbed on the clay mineral surface by the adsorption of ammonium ions. The adsorption mechanism of ammonium ion on the alumina surface and silica surface of kaolinite with and without water was studied using quantum chemistry calculation method based on density functional theory. The results showed that ammonium ions are most likely to adsorb around the lying hydroxyl groups on the alumina surface and the centre of the six-membered ring on the silica surface. Ammonium ions were mainly adsorbed onto the kaolinite surface by electrostatic interaction and hydrogen bonding. The presence of water molecules can make the adsorption energy of ammonium ions on the alumina surface decrease greatly, but little change on the silica surface. Ammonium ions were more easily adsorbed on the silica surface. The adsorption energy of ammonium ions on the kaolinite in the presence of water was less than that of rare earth lanthanum ions.