Clay minerals in soils and rocks exhibit large volume change upon interaction with water and this behavior becomes even more complex when the strata are being stressed by the engineering and environmental loads. Therefore, a realistic prediction of the hydro-mechanical behavior of the clay-bearing strata is always a challenge due to their coupled swelling-mechanical response in the cases of geotechnical and geoenvironmental engineering problems, nuclear waste storage in clay-bearing rock repositories, shale gas extraction, and other uses of clay in the manufacturing industry. All the existing behavior models have restricted applications in the engineering and other fields of practice mainly due to the partial consideration of the structure and fabric of clay-bearing strata in the model formulation. In this study, a hydro-mechanical behavior model has been formulated using the parameters acquired from the molecular-level simulations and modeling of the volume change and stress–strain behavior of the clay-bearing structure. The Molecular Mechanics and Molecular Dynamic simulations were performed on the natural structure of the clay-bearing strata formulated using Monte Carlo technique. The mathematical model, developed from the simulation results, can predict the overall hydro-mechanical behavior of clay-bearing strata for all possible combinations of clay minerals, non-clay minerals, salts causing cementation of the soil/rock structure, confining pressures, and the induced strain levels. The developed model has successfully been validated through laboratory and field testing on the clay-bearing strata in both the elastic and elasto-plastic regions of the stress–strain behavior and also from the data of two (02) swelling clays (MX-80 and FEBEX Bentonite) from the existing literature, supporting the universal nature of the developed behavior model.