This paper proposes a novel methodology for understanding the meso-scale aggregation of clay platelets in water. We use Molecular Dynamics simulations using the CLAYFF force fields to represent the interactions between two layers of Wyoming montmorillonite (Na-smectite) in bulk water. The analyses are used to establish the potential of mean force at different spacings between the layers for edge-to-edge and face-to-face interactions. This is accomplished by finding the change in free energy as a function of the separation distance between the platelets using thermodynamic perturbation theory with a simple overlap sampling method. These nanoscale results are then used to calibrate the Gay–Berne (GB) potential that represents each platelet as a single-site ellipsoidal body. A coarse-graining upscaling approach then uses the GB potentials and molecular dynamics to represent the meso-scale aggregation of clay platelets (at submicron length scale). Results from meso-scale simulations obtain the equilibrium/jamming configurations for mono-disperse clay platelets. The results show aggregation for a range of clay platelets dimensions and pressures with mean stack size ranging from 3 to 8 platelets. The particle assemblies become more ordered and exhibit more pronounced elastic anisotropy at higher confining pressures. The results are in good agreement with previously measured nano-indentation moduli over a wide range of clay packing densities.