The numerical modeling and simulation have been used increasingly as tools for examining and interpreting the bulk structure and properties of materials. The use of molecular dynamics (MD) simulations to model the structure of materials is now both widespread and reasonably well understood. In this research, we introduced the numerical method to calculate the physico-chemical properties such as a diffusion coefficient and a viscosity of clay mineral. In this research, a series of MD calculations were performed for clay mineral and clay-water systems, appropriate to a saturated deep geological setting. Then, by using homogenization analysis (HA), the diffusion coefficients are calculated for conditions of the spatial distribution of the water viscosity associated with some configuration of clay minerals. This result of numerical analysis is quite similar to the previous experimental results. It means that the introduced numerical method is very useful to calculate the physico-chemical properties of clay minerals under various environmental conditions.