Heap bio-leaching technology is extensively applied to recover metals from low-grade complex ores in the mining industry, particularly the copper sulfide ores. Understanding the effect of bio-leaching process on the pore structure of packed particle beds is important to enhance the percolation and leaching performances with respect to design and operation of heap leaching system. The porosity, pore size distribution and degree of pore connectivity are the three most important features correlated with fluid flow in heap leaching operation. In this study, a spiral X-ray CT scanner, combined with 3D imaging and analysis, was used to characterize the complex pore structure of the packed ore particle beds before and after bioleaching copper sulfide ores. The results indicate that the pore structure has temporal and spatial variations during bio-leaching process.