Abstract: Bioleaching technology, a method used in mining, utilizes organisms or microorganisms to dissolve and leach useful components from ore. This technology is applied widely in many countries in mining and production of various metals. Although considerable economic benefits have been obtained with the help of bioleaching technology, this technology faces many challenges. For example, as the leaching process progresses, the permeability of the ore heap is worsened from the presence of fine particles and muddy ore. As such, improving heap permeability is a key focus in the field of leaching mining technology. Agglomeration technology, an effective method for improving the permeability of ore heaps, involves crushing the ore and agglomerating it with binders before leaching, which alters the structure of the ore, especially ore powder. The resulting granular structure provides space for the flow of the solution and greatly improves the permeability of the leaching system. The pore structure is constantly changing as the leaching process progresses, which affects the seepage of the solution and even the effect of leaching the ore. In this study, leaching tests were conducted using single-ore granulation of secondary copper sulfide ore powder, binders, and NaCl. Changes in the pore structure during leaching were investigated using X-ray computerized tomography, digital image processing, and three-dimensional reconstruction methods. In addition, COMSOL Multiphysics simulation software was used to construct a simulation model of the flow of the solution in the pore channels. The results reveal that the number, average volume, average surface area, and average equivalent diameter of pores inside the granulated ore increase respectively by 99%, 151%, 223%, and 90%. In addition, the porosity increases fourfold and the pore connectivity nearly triples. The flow velocity and pressure of the solution was found to increase sharply as the solution flows through the narrow and bottom areas of the pore channels, which has a great impact on the stability of the ore granulation structure.