The random and heterogeneous pore structure is a significant factor that dominates physical and mechanical behaviors of soils such as fluid flow and geomechanical responses driven by loading. The characterization method using non-destructive testing such as micro X-ray CT technique which has a high resolution with micrometer unit allows to observe internal structure of soils. However, the application has been limited to qualitatively observe 2D and 3D CT images and to obtain the void ratio at macro-scale although the CT images contain enormous information of materials of interests. In this study, we constructed the 3D particle and pore structures based on sequentially taken 2D images of glass beads and quantitatively defined complex pore structure with void cell and void channel. This approach was enabled by implementing image processing techniques that include coordinate transformation, binarization, Delaunay Triangulation, and Euclidean Distance Transform. It was confirmed that the suggested algorithm allows to quantitatively evaluate the distribution of void cells and their connectivity of heterogeneous pore structures for glass beads.