In-situ leaching based on NH4+ is commonly employed for the separation and extraction of rare earths. However, the residual ammonium salt is affiliated on clay minerals, and liable to be leached out which poses a serious threat to the aquatic environment. To better develop the leaching agents for rare earth extraction based on ammonium ions, some fundamental data on the interaction between NH4+ and minerals must be investigated. This study explores the adsorption mechanism of the primary constituent minerals of rare-earth ores on ammonium ions. According to the density functional theory (DFT) calculations via first principles, the plane of montmorillonite (0 0 1), halloysite (0 0 1), kaolinite (0 0 1), kaolinite (0 0 −1), illite (0 0 1) and illite (0 1 0) electron density difference in the adsorption process shows that NH4+ is adsorbed on the surface of clay minerals by electrostatic action and hydrogen bonding, and the average adsorption energy of NH4+ is in the order of montmorillonite > halloysite > illite > kaolinite. Correspond with the theoretical results, the experiments testified the microscopic mechanism of NH4+ adsorption. The residual ammonium salts in weathered crust leaching rare earth ores are adsorbed on montmorillonite, halloysite, illite and kaolinite with a capacity of 0.56, 0.45, 0.38 and 0.34mg/L, respectively. Most of the absorbed ammonium on clay minerals was found to be with the water-soluble state rather than ion-exchange state. These water-soluble forms can be efficiently eluted by disrupting their interface interactions to leach out.