This research addresses the need for a multiscale model for the determination of the thermophysical properties of nanofiller-enhanced thermoset polymer composites. Specifically, we analyzed the thermophysical properties of an epoxy resin containing bisphenol-A diglyceryl ether (DGEBA) as an epoxy monomer and dicyandiamide (DICY) and diethylene triamine (DETA) as cross-linking agents. The cross-linking process occurs at the atomistic scale through the formation of bonds among the reactive particles within the epoxy and hardener molecules. To derive the interatomic coarse-grained potential for the mesoscopic model and match the density of the material studied through atomic simulations, we employed the iterative Boltzmann inversion method. The newly developed coarse-grained molecular dynamics model effectively reproduces various thermophysical properties of the DGEBA-DICY-DETA resin system. Furthermore, we simulated nanocomposites made of the considered epoxy additivated with graphene nanofillers at the mesoscopic level and verified them against continuum approaches. Our results demonstrate that a moderate amount of nanofillers (up to 2 wt.%) increases the elastic modulus and thermal conductivity of the epoxy resin while decreasing the Poisson’s ratio. For the first time, we present a coarse-grained model of DGEBA-DICY-DETA/graphene materials, which can facilitate the design and development of composites with tunable thermophysical properties for a potentially wide range of applications, e.g., automotive, aerospace, biomedical, or energy ones.