A lightweight composite with outstanding damping effects and impact resistance is significant for the design of functional structures in advanced equipment, such as aircraft and space vehicles. In this paper, the mechanical properties of solution-blended graphene nanoplatelets (GNPs)/polyether-ether-ketone (PEEK) nanocomposites were characterized by both experimental and numerical methods. It can be found that the layer number and packing configuration of graphene layers are critical to the efficiency of energy dissipation in the composite, while a pack of six- layer graphene and the perpendicular arrangement to the shockwave direction provide the most outstanding energy dissipation ability. The reflection of shockwave caused by graphene reinforcements in the nanocomposite was found to be the dominating reason for the enhanced energy dissipation effect. Physical mechanisms of energy dissipation are investigated by a molecular modeling method to provide insights into the cross-scale design of graphene-reinforced nanocomposites as structural materials.