The objectives of this study are, 1) to simulate asphalt binder modified with exfoliated multi-layered graphite nanoplatelets (xGNP) using the Molecular Dynamics (MD) method, and 2) to analyze different modulus properties of these asphalt binder models compared with those of the control asphalt binder model. The multi-layered graphene model was used to represent the xGNP particles, which were used to modify the control asphalt in the laboratory. The three-component control asphalt binder model was used as in the authors’ previous study. The xGNP modified asphalt binder model was built by incorporating the xGNP model and control asphalt binder model and controlling mass ratios to represent the laboratory prepared samples. After the xGNP modified asphalt binder model was generated, the densities of the control and xGNP modified asphalt binder models were computed and verified. Mechanical properties of these models were simulated and calculated in MD simulations using procedures similar to those in the experiments, which include the bulk modulus, Young’s modulus, shear modulus and Poisson’s ratio. The simulation results indicate that the temperature-modulus trends of these asphalt binder models were comparable to those of the laboratory data. The MD simulation data were larger than the laboratory results due to limitations of the current MD simulation, which are discussed in this study. In addition, Poisson’s ratios calculated from the MD simulations coincided with the laboratory results.