The ionic rare earth (RE) ore body undergoes particle transport and pore structure change during the leaching process, resulting in "uneven percolation, preferential channel, leaching blind area," and other problems, leading to structural changes in the ore body, low leaching efficiency, and waste of resources. The unsaturated infiltration process is also the key stage that causes these problems. The initial pore structure evolution of the ore body plays a decisive role in the permeability coefficient of the ore body, and the direct influencing factor of the permeability coefficient is the distribution of the pore radius. We carried out research through indoor simulated leaching, the filter paper method for determining matrix suction, and nuclear magnetic resonance (NMR) testing. An ionic rare earth ore soil-water characteristic curve within a large matrix suction range was obtained by the filter paper method. With the increase in volumetric water content, the matrix suction presents a sharp downward trend. When the volumetric water content is less than 20%, this rule is particularly obvious. With the increase in matrix suction, the thickness of the adsorbed water film on the particle surface and pore radius show a decreasing power function trend. Under percolation, the porosity of an ionic rare earth ore sample tends to increase linearly with the increase in volumetric water content during the process from non-saturation to saturation; the porosity of a saturated ore sample after seepage expanded by 17.5 times compared to that of an unsaturated ore sample before seepage. The change rule of the internal microstructure of the ore sample is reflected in the gradual disappearance of micro pores and the gradual formation of small, medium, large, and mega pores, which shows a gradual increase trend. In the pore radius distribution, the more large and medium pores, the larger the permeability coefficient; the more micro and small pores, the smaller the permeability coefficient. For some ore bodies with poor permeability, the ore body is infiltrated with clear water under small water pressure before leaching with a leaching solution, which can improve the permeability of the ore body, effectively improve the efficiency of rare earth leaching, and increase the economic benefits.