Expansive soils are known to be hazardous materials for infrastructure due to their high shrinking or swelling potential. Understanding the shrinking factors of expansive soils such as montmorillonite (MMT) is essential for predicting their mechanical properties. The interactions between the components of Na-MMT clays, e.g., MMT layer–layer (LL), layer–cation (LC), layer–water (LW) and water–cation (WC), are responsible for its shrinking behavior. In this study, molecular dynamics simulation and grand canonical Monte Carlo simulations are used to investigate the interaction energy evolution in the layered structure of Na-MMT for the shrinkage mechanisms analysis of clay. The results of simulation indicate that the magnitude of the interaction energy contributed by the interlayer cations dehydration is the driving force of the interlayer shrinkage. Furthermore, in the hydrated state, with one water layer, two water layers and three water layers, the attractive interactions between WC and LW, maintain the stability of the clay layers. However, at the dry state, the interaction energy between layers and cations appears to be the most essential component in holding the stacked layers together, which provides structural stability to the clay sheets. Finally, the study reveals that intermolecular interactions contribute to the mechanical properties of clays such as cohesive and elastic properties.