In long-term consolidation process, bentonite shows secondary and tertial stages. Bentonite is a microinhomogeneous material consisting of mainly nanometer scale of smectite clay minerals, micron scale of macro-grains, water, and air. One smectite mineral is a platelet or lamella. Several minerals are piled up and form a stack. In saturated bentonite, water exists both in the interlayer space of stacks and in external pores. The interlayer water is chemically active. Here, we first present experimental results of an in situ X-ray diffraction (XRD) analysis during consolidation process. The data suggest that at the first stage of consolidation, water is drained from external pores, and at the secondary stage, the interlayer water is drained. Second, molecular dynamics (MD) analyses are applied to specify local properties of hydrated smectite. We also show that by MD the secondary consolidation is not caused by visco-elastic characteristics of clay skeleton. Third, we present a multiscale homogenization analysis (HA) method applied to the seepage behavior of bentonite. Here, the local property of water viscosity calculated by MD is used. Fourth, the results of permeability change are introduced in a 1-D finite strain consolidation analysis, which can represent the secondary consolidation behavior. And if multicharged anions are infiltrated, the chemical properties of bentonite are drastically changed. This causes a change of permeability. This is a major factor of the tertial consolidation. We discuss an analysis method of tertial consolidation because of this permeability change.