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When drilling for oil and gas, maintaining wellbore stability is of primary importance to reduce non-productive time and trouble cost. Shale swelling causes many problems related to stability when drilling with water-based drilling fluids (WBDF). For many years, it remains the number one cause of time wastage and well abandonment. Different shale samples have different chemical compositions that affect their behavior when in contact with water. This factor makes laboratory-based analysis and characterization of the swelling mechanisms and action of swelling inhibitors extremely challenging. Moreover, the need to replicate different conditions at which clay–water interactions might occur necessitates using a different technique. Molecular dynamics (MD) simulation can be used as a supplement technique to help interpret experimental studies, test and improve a theoretical model, and provide empirical data in high-pressure and high-temperature condition of the borehole. MD simulation applies Newton’s second law of motion to describe particles’ movement in a classical system. The technique can be performed on the time scale of nanoseconds, and in three dimensions, it is thus sufficient for the study of clay–water interaction at a molecular level. It provides a unique view of the clay mineral interlayer and surface activities. This work reviews the progress in MD simulations of clay swelling and its inhibition mechanisms for application in petroleum drilling operations.