This paper presents systematic molecular dynamics modelling of Na-montmorillonite subjected to uniaxial compression and unidirectional shearing. An initial 3D model of a single-cell Na-montmorillonite structure is established using the Build Crystal module. The space group is C2/m, and COMPASS force fields are applied. Hydration analysis of Na-montmorillonite has been performed to validate the simulation procedures, where the number of absorbed water molecules varied with respect to the various lattice parameters. A series of uniaxial compression stress σzz and unidirectional shear stress τxy values are applied to the Na-montmorillonite structure. It is shown that the lattice parameter and hydration degree exhibit significant influence on the stress–strain relationship of Na-montmorillonite. The ultimate strain increases with increases in the lattice parameter but decreases in the number of water molecules. For saturated Na-montmorillonite, more water molecules result in a stiffer clay mineral under uniaxial compression and unidirectional shearing.