The objective of this investigation was to elaborate on the influence of grain boundaries on the interfacial thermal conductance between bi-crystalline graphene and polyethylene in a nanocomposite. Reverse non-equilibrium molecular dynamics simulations were implemented in combination with Lennard-Jones and reactive force field interatomic potential parameters. According to the simulation results, high-energy grain boundary atoms in bi-crystalline graphene played a substantial role in enhancing the interfacial thermal conductance values. To further illuminate the mechanisms of enhanced graphene–polyethylene interfacial thermal conductance in the presence of grain boundaries, a systematic study on the vibrational density of states and structural evolution was also performed. It was found that the vibrational coupling between bi-crystalline graphene and the polymer was enhanced; whereas a decline in the radial density profile and coordination number resulted in a shifting of the in-plane vibrational modes such that they amalgamated with those of the polyethylene matrix. Thus, bi-crystalline graphene can be considered to be a superior potential reinforcement for nanocomposites as compared to the pristine configuration for applications in thermoelectric and thermal interface materials.