This paper is concerned with microstructure modeling and analysis of porous scaffolds fabricated by the salt-leaching method. 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. Subsequently, finite element meshes of microstructures of pores are generated and the effective diffusivity of porous scaffolds is predicted using the finite element method. From the numerical results, it is demonstrated that the volume fractions and configurations of salt particles affect the effective diffusivity that can represent cell-culture characteristics.