Polyurethanes (PU) are commonly used in transparent armor systems to increase the survivability, blast resistance, multi-hit resistance and fragment containment of multilayered systems. The high tensile-ductility, fracture toughness and self-healing ability are key factors that determine the performance of polyurethanes under high-strain rate conditions. However, so far it is not clear how the macromolecular structural features influence the failure mechanism of PU under dynamic loading conditions. Here, Halloysite nanotubes-reinforced polyurethane nanocomposites are produced that dramatically improve the macromolecular structure's ability to resist fracture. A low content of Halloysite nanotubes (HNTs) (maximum 0.8 wt.%) was introduced in the polyurethane to investigate the effect of the nanotubes on the resultant micro-domain morphological architecture. Gas-gun spall testing results showed an increase of 35% in spall strength and 21% fracture toughness for the nanocomposite. Subsequent characterization results show present the influence of the HNTs to alter the resultant hard domain spherulitic structure, which leads to a more energy dissipative fracture mechanism characterized by a rougher fracture surface with highly deformed interspherulitic regions. Analysis of the free-surface velocity histories, combined with fractographies of the spalled surfaces provides information about the failure mechanism and fracture kinetics. The spherulites present a brittle fracture character, while the interspherulitic regions present a ductile behaviour with large deformation. Ballistic testing on multilayered glass/polymer plates (transparent armour configuration) results showed an increase in the ballistic limit, from 457 to 491 m/s, with the change from a neat polyurethane interlayer to the nanocomposite. A higher degree of phase separation was detected within the structure of the nanocomposite, indicating that the presence of the HNTs increases the chemical incompatibility of the hard and soft segments of the polyurethane. Molecular dynamics simulations were conducted to further investigate the effect of HNTs on the immiscibility and mobility of the segmented structure of the polyurethane. These results demonstrate that the significant improvement in the ballistic performance of the nanocomposite interlayers were not due to the small concentration of HNTs acting as simple reinforcing phase, but rather their influence in the formation of the micro-structure of the matrix polymer.