The scaffolds are used to regenerate the damaged tissues of cartilages and bones growing the patients’ cells. In particular, it is very important that the pores of scaffolds are connected to one another without interruption because they serve as channels for supplying oxygen or various nutrients required for cell growth to the tissue cells. To model the pores and their interconnectivity generated by leaching cubic salt particles, packing and compression processes of salt particles are simulated using the discrete element method. Based on the pore configurations obtained using the discrete element simulations, the domains through which the oxygen and nutrients flow are modeled and the diffusion analyses are then conducted to evaluate the scaffold performance in an indirect manner. The effect of the size and mass of salt on the scaffold is investigated by calculating one- and three-dimensional effective diffusivities. It is confirmed that a high diffusivity is obtained with a high level of pore connectivity, which would lead to good performance of cell growth.