Polymer/clay nanocomposites (PCNs) are multi-functional materials that have superior mechanical and thermal properties than polymer-based materials while maintaining their characteristic properties of lightweight and optical clarity. These materials are obtained by adding small amounts of clay nanofillers to a polymer matrix. In this work, we proposed a molecular model to investigate the morphology and thermomechanical properties of thermosetting clay nanocomposites. The epoxy matrix was composed of several representative cross-linked epoxy units, and different structures of PCNs, which correspond to intercalated or exfoliated status, were considered by varying the amount of polymer phase in the interlayer space. Molecular dynamics simulations of different nanocomposite structures were used to provide atomistic insights into the arrangement of the constitutive components of PCNs, the molecular interactions occurring in the interphase zone, and the influence of silicate layer on the thermodynamic and elastic properties of these multi-functional materials