Recent advances in experimental techniques have enabled impact tests of ultrathin films. For example, microprojectile impact tests of ultrathin polymer films have revealed that their specific penetration energy is about ten times more than that of the conventional armor materials. On the other hand, metallic nanostructures have demonstrated extraordinary mechanical properties. These observations suggest that multilayer arrangements of nanoscale polymer and metal films could possess superior ballistic impact resistance. In order to test this hypothesis, we simulated the impact tests of multilayer aluminum-polyurea nanostructures using molecular dynamics (MD). Our simulations demonstrate that the ballistic limit velocity (V50) and the specific penetration energy of the multilayers and aluminum nanofilms are significantly higher than the experimentally measured values for any material. In order to further investigate the mechanisms associated with the observed superior ballistic performance of multilayers, we computed their V50 using an existing membrane model and another analytical model reflecting a two-stage penetration process. Our results demonstrate a potential bottom-up design pathway for developing flexible barrier materials with superior dynamic penetration resistance.