Abstract: Ion-adsorption rare earth (RE) ore is a typical kind of rare earth ore derived from the weathering crust of igneous rocks. Variation in permeability of ion-adsorption rare earth ore is one of the indicative factors of mining efficiency. Permeability of the RE ore is controlled by its pore structure. Previous studies mainly kept on the RE ores in completely weathered zones, little on those in the zones with other weathering degrees. With the exhaustion of rare earth resources in the completely weathered zone, the extraction of the RE ore from the zones with other weathering degrees has gained more attention from the industrial sectors. This study shows a study on variations in pore structures and permeabilities of the RE ores in the zones with different weathering degrees, including the residual soil and completely weathered and highly weathered zones. The undisturbed samples were taken from an un-mining section of the Zudong mining area in Jiangxi province. Simulated in situ leaching experiments were conducted on the samples to measure their permeability coefficients before and after leaching. X-ray computer tomography scanning techniques were applied to the capture structure of the samples before and after leaching, and image processing techniques were used to construct their three-dimensional pore structure and extract their pore structure parameters. Variations in pore structure parameters and permeability coefficients of the RE ores from the zones with different weathering degrees were then carried out by a quantitatively comparative analysis. The results indicate that (1) the variation rate in permeability coefficient, and the pore structure parameters, including porosity, connectivity, and average coordination number, decrease with the decrease in weathering degree. Notably, these variation rates for the RE ores in the highly weathered zone are the smallest, indicating the RE ores in this zone are more leachable than those in residual soil if their abundance is not much different. (2) The mechanism leading to their differences was further investigated by the analyses of particle size distribution and mineralogical composition before and after leaching. The analysis results indicate that the differences in their variation of pore structure and permeability among the RE ore in the zones with different weathering degrees are caused by the differences in followings during leaching, including the chemical decomposition of plagioclase and mica, ion exchange, and disaggregation.The results can provide reference for the full development and utilization of similar ion-adsorption rare earth ore.