Nanostructured composites inspired by structural biomaterials such as bone and nacre form intriguing design templates for biomimetic materials. Here we use large scale molecular dynamics to study the shock response of nanocomposites with similar nanoscopic structural features as bone, to determine whether bioinspired nanostructures provide an improved shock mitigating performance. The utilization of these nanostructures is motivated by the toughness of bone under tensile load, which is far greater than its constituent phases and greater than most synthetic materials. To facilitate the computational experiments, we develop a modified version of an Embedded Atom Method (EAM) alloy multi-body interatomic potential to model the mechanical and physical properties of dissimilar phases of the biomimetic bone nanostructure. We find that the geometric arrangement and the specific length scales of design elements at nanoscale does not have a significant effect on shock dissipation, in contrast to the case of tensile loading where the nanostructural length scales strongly influence the mechanical properties. We find that interfacial sliding between the composite’s constituents is a major source of plasticity under shock loading. Based on this finding, we conclude that controlling the interfacial strength can be used to design a material with larger shock absorption. These observations provide valuable insight towards improving the design of nanostructures in shock-absorbing applications, and suggest that by tuning the interfacial properties in the nanocomposite may provide a path to design materials with enhanced shock absorbing capability.