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Materials commonly involve microstructure. Clay is a microinhomogeneous material with nanoscale microstructure. Key issues to understand the behavior of such a finely microinhomogeneous material are as follows: the microstructure is characterized in detail, the local distribution of material properties is identified by experiment or simulation, and the microscale characteristics are related to the macroscale behavior by a seamless manner. For characterizing a microstructure of bentonite, we introduce a conforcal laser scanning microscope (CLSM) together with SEM. By CLSM we can specify a 3D configuration under atmospheric condition. Properties of water‐saturated bentonite are mainly controlled by hydrated montmorillonite, which is the major clay mineral of bentonite. Smectite minerals including montmorillonite are extremely fine and poorly crystallized, so it is difficult to determine the properties by experiment. We inquire into the physicochemical properties by a molecular dynamics simulation method. Then, we develop a multiscale homogenization method to extend the microscopic characteristics to the macroscopic behavior. We show numerical examples of a diffusion problem.