Molecular dynamics (MD) simulation-based development of heat resistance nanocomposite materials for nanoheat transfer devices (like nanoheat exchanger) and applications have been studied. In this study, MD software (Materials Studio) has been used to know the heat transport behaviors of the graphene-reinforced thermoplastic polyurethane (Gr/TPU) nanocomposite. The effect of graphene weight percentage (wt%) on thermal properties (e.g., glass transition temperature, coefficient of thermal expansion, heat capacity, thermal conductivity, and interface thermal conductance) of Gr/TPU nanocomposites has been studied. Condensed-phase optimized molecular potentials for atomistic simulation studies (COMPASS) force field which is incorporated in both amorphous and forcite plus atomistic simulation modules within the software are used for this present study. Layer models have been developed to characterize thermal properties of the Gr/TPU nanocomposites. It is seen from the simulation results that glass transition temperature (Tg) of the Gr/TPU nanocomposites is higher than that of pure TPU. MD simulation results indicate that addition of graphene into TPU matrix enhances thermal conductivity. The present study provides effective guidance and understanding of the thermal mechanism of graphene/TPU nanocomposites for improving their thermal properties. Finally, the revealed enhanced thermal properties of nanocomposites, the interfacial interaction energy, and the free volume of polymer nanocomposites are examined and discussed.