The results from mesoscale simulations of the formation and evolution of microstructure for assemblies of Na-smectite particles based on assumed size distributions of individual clay platelets are presented here. The analyses predicted particle arrangements and aggregation (i.e. platelets linked in face–face configurations) and are used to link geometric properties of the microstructure and mechanical properties of the particle assemblies. Interactions between individual ellipsoidal clay platelets are represented using the Gay-Berne potential based on atomistic simulations of the free energy between two Na-smectite clay-platelets in liquid water, following a novel coarse-graining method developed previously. The current study describes the geometric (aggregate thickness, orientation, and porosity) and elastic properties in the ‘jammed states’ from the mesoscale simulations for selected ranges of clay particle sizes and confining pressures. The thickness of clay aggregates for monodisperse assemblies increases (with average stack thickness consisting of n = 3–8 platelets) with the diameter of the individual clay platelets and with the level of confining pressure. Aggregates break down at high confining pressures (50–300 atm) due to slippage between the platelets. Polydisperse simulations generate smaller aggregates (n = 2) and show much smaller effects of confining pressure. All assemblies show increased order with confining pressure, implying more anisotropic microstructure. The mesoscale simulations are also in good agreement with macroscopic compression behavior measured in conventional 1-D laboratory compression tests. The mesoscale assemblies exhibit cubic symmetry in elastic properties. The results for larger platelets (D = 1000 Å) are in good agreement with nano-indentation measurements on natural clays and shale samples.