Interfaces between graphene play a crucial yet poorly understood role in the transport of heat in graphene-based composite materials. The primary focus of this study was on developing a quantitative understanding of the mechanism underlying the heat flow through the structure of a graphene-based polymer matrix composite material. The macroscopic thermal properties of the composite material were studied to provide an effective way to improve thermal conductivity for polymers. Molecular dynamics simulations were performed to understand the thermal resistance of interfaces between graphene and to optimize the condition of the interface for nanoscale thermal reinforcement. A modified Maxwell Garnett effective medium theory was used to predict the thermal conductivity of the composite material. The results indicated that the thermal properties of a graphene-based polymer matrix composite material depends upon the details of the microscopic structure and atomic interactions within the composite material. Interfaces between graphene contribute significantly to the thermal conductivity of the composite material. This is even more critical for composite materials where the lateral size of graphene can affect the thermal performance of the composite material significantly. Low thermal boundary resistance and high thermal conductivity can be achieved by introducing the structure of a carbon cross-link network between graphene. The proper combination of graphene with large size and carbon cross-links with high density can lead to a fifty-fold improvement in overall thermal performance for the polymer matrix composite material. The relative position between graphene can be adjusted for the further optimization of interfacial conditions, but with little success in nanoscale thermal reinforcement. The bulk thermal conductivity of graphene nanoribbons has been found to be about 2570 W/m·K at room temperature. The results can provide a theoretical basis for understanding the applied physics of thermal transport at the nanoscale in graphene-based polymer matrix composite materials.