The molecular dynamics simulation was used to study and design a polymer composites system with excellent mechanical strength and less heat generation in a dynamic process. A series of system factors such as filler loading, surface modification onto filler, and network of cross-linking filler particles on mechanical and heat generation of polymer composites are systematically considered. It is found that the surface grafting onto fillers can restrain the heat generation of polymer composite in the dynamic process, while it shows less effect on the mechanical property. A network of cross-linking filler particles can be fabricated by a combination of grafting chains onto fillers. By filling such a network into the polymer, the mechanical and heat generation properties of polymer composites are significantly improved. Simulation results can help experimental fabrication of polymer composites with excellent mechanical and heat generation properties.