In order to investigate the influence of the ion exchange process on the permeability of rare earth ore bodies in the leaching process, a laboratory-scale comparative experiment with ammonium sulfate solution and deionized (DI) water as leaching solutions is conducted. Compared with the DI water leaching test, the permeability coefficient of the rare earth ore sample leached by the ammonium sulfate solution gradually decreases at the beginning and then increases with the completion of leaching. The physical and morphological evolutions of rare earth ore samples in this comparative experiment are also monitored by nuclear magnetic resonance and scanning electron microscopy. It is concluded that the change in the permeability coefficient arises from the adsorption–desorption of a large number of clay microparticles, resulting in a dynamic evolution of pore structures. Further mechanism analysis suggests that the change in internal ionic strength caused by ion exchange and leaching solution seepage promotes the adsorption–desorption behavior of clay microparticles.