Abstract: Heap leaching has been widely used in mining low-grade sulfide copper minerals because of its outstanding advantages of low cost, fast infrastructure, and effective recovery. However, the segregation and stratification of crushed ore feeds during the dumping and stacking process of heap leaching are significant and prone to occur, leading to preferential flow paths and low heap leaching efficiency. Based on the complex segregation and layered structure of the heap leaching system, combined with X-ray CT nondestructive detection, morphological open operation processing, MATLAB and OsiriX visualization software, and other means, the key characterization parameters, such as the equivalent pore size, area, and number of pores between particles, are introduced. This study explores the intergranular pore structure characteristics and evolution regulation of the leaching system from the perspective of two-dimensional quantification and three-dimensional visualization. This study found that the fine interlayers are in the shape of “inclusions” and are inside the coarse ore particles. The analysis demonstrates that it is an important cause of particle segregation and stratification in the heap leaching system. The migration of fine particles under the action of ore leaching leads to sedimentary compaction, which decreased from 197 mm to below 180 mm. After 21 days of ore leaching, the pores in the upper and lower parts of the ore heap showed increasing and decreasing trends, respectively. In addition, the diameter of the longitudinal equivalent pores decreased from 2.81 to 2.18 mm; the change trend and extent were considerably greater than the equivalent diameter of the transverse intergranular pores. When comparing the three-dimensional intergranular pore structures of the column leaching system for 0 and 21 days of ore leaching, it is evident that the fine particle interlayer is located in the bonding and aggregation region. The peripheral area of the fine particle interlayer also forms the circumvention and dominant flow path of the solution. This suggests the coexistence of hydraulic erosion and reactive dissolution in the heap leaching system. The combined effect of these processes leads to bonding and aggregation in the area where the fine particle interlayer is located, forming solution and dominant flow paths in the area surrounding the fine particle interlayer. These preferential flow paths may result in the solution not actually participating in the leaching reaction and leaving the heap leaching system, which is undesirable and should be avoided in real heap leaching systems.