A hierarchical procedure bridging the gap between atomistic and mesoscopic simulation for polymer-clay nanocomposite (PCN) design is presented. The dissipative particle dynamics (DPD) is adopted as the mesoscopic simulation technique, and the interaction parameters of the mesoscopic model are estimated by mapping the corresponding energy values obtained from atomistic molecular dynamics (MD) simulations. The predicted structure of the nylon 6 PCN system considered is in excellent agreement with previous experimental and atomistic simulation results.