Since their rapid adoption over the last two decades, polyurea elastomer coatings have become an essential component in ballistic protection materials and armor coatings. Polyurea’s copolymer architecture forms microphase separated nanostructures of “hard” and “soft” domains that are rich and poor in hydrogen-bond forming isocyanate groups. Experiments have correlated this hierarchy of domains with improved shock mitigation, but it remains unclear whether the atomic-scale bonds that drive self-assembly or the mesoscale domains that are produced by it play a larger role in shock mitigation. In this study, we apply molecular dynamics simulations to model shock impact and propagation in nanostructured polyurea. We monitor shock propagation through polyurea’s hard and soft domains and shock transmission and reflection at hard/soft domain interfaces. We observe that while shocks do trigger the breaking of a substantial number of hydrogen bonds in polyurea’s hard phase, the sudden compression also dramatically slows hard phase molecular diffusion, delaying bond breaking until after the shock front has left the vicinity of the front. This suppression of molecular motion reduces the influence of hydrogen bond breaking on shock propagation while enhancing the mechanical mismatch at hard and soft domain interfaces.