A fundamental concept combining a molecular behavior and macro-continuum phenomenon is presented for a multicomponent solute diffusion problem in bentonite clay, which is a key component of the Engineering Barrier System (EBS) of high-level radioactive waste disposal (HLRW). Bentonite is a micro-inhomogeneous material. Properties of the saturated bentonite are characterized by the constituent clay mineral (montmorillonite) and water, namely montmorillonite hydrate. We analyze its molecular behavior by applying a molecular dynamics (MD) simulation to inquire into the physicochemical properties such as diffusivity of chemical species. For extending the microscopic characteristics of constituent materials to a macroscopic diffusion behavior of the micro-inhomogeneous material we apply a homogenization analysis (HA).