In-situ leaching is essential for mining rare earth elements (REEs) from ion-adsorption rare earth (RE) ores. The efficiency of RE mining is dependent on the permeabilities of ion-adsorption RE ores, and the permeabilities are controlled by their pore structures. However, the current understanding of the pore structures and permeabilities of the RE ores during leaching is limited, particularly their dynamic variations, the controlling roles of different pore structure parameters on the permeability, the roles of the influencing factors and the mechanisms causing the variations. To investigate the above-mentioned issues, we conducted an experimental study of simulated in-situ leaching on undisturbed ion-adsorption RE ore samples under different conditions via constant waterhead permeability tests. The leaching conditions included leaching time, concentration and waterhead of the (NH4)2SO4 solution. Three-dimensional (3-D) pore structures of the RE ores before, during, and after leaching were constructed via X-ray computed tomography, and their pore structure parameters were measured using 3-D image computation. It was observed that the dynamic variations in both the pore structure parameters and permeability coefficients of the RE ores occurred in three distinct stages: rapid reduction, less rapid reduction, and little reduction. The experimental results also revealed that the permeability coefficients of the RE ores were primarily dependent on the average coordination number among the seven pore structure parameters examined, and that the pore throats larger than 30 μm in diameter served as the most effective seepage channels within the RE ores. The waterhead of the leaching solution had a stronger influence on the variations in pore structures and permeabilities compared to that of the concentration. Analysis of the particle/aggregate size distribution and mineralogical compositions of the RE ores before and after leaching indicated that the decreases in the pore structure parameters and permeabilities were largely attributed to clogging of the pore throats and pores by migrated and newly formed clays, as well as swelling of the latter. The newly formed clays were the products of the decomposition of K-feldspar and mica resulting from chemical reactions with the leaching solution. The clays from the two sources occurred in disaggregated and aggregated forms. The results of this study provide an important reference for the mining of RE ores via leaching.