It is technically challenging, but critically important, to calculate the in situ 3D nano- and microscale strain and reorientation patterns in hierarchical nanocomposite materials. Doing so can illuminate the mechanisms enabling multiple functional optimization in biological composites, as well as test the functionality of bioinspired materials. Here we developed a novel 3D nanofibrillar orientation reconstruction method to determine deformation mechanisms at the nano- and microscale in stomatopod cuticle - a material adapted for high dynamic mechanical resistance - which combines synchrotron microbeam X-ray diffraction with in situ deformation and fibre-composite theory. Stomatopod cuticle consists of mineralized chitin nanofibers in a mineral and protein matrix, assembled in the form of parallel plywood (Bouligand) layers and interpenetrating pore-canals at the microscale. The angularly-resolved in situ deformation and reorientation of chitin nanofibers at different strain rates were studied. We revealed anisotropic deformation inside Bouligand lamellae, non-monotonic response of fibre strain with increasing strain rate, spatial gradients in fibre strain on flexion, accompanied by load-induced fibre reorientation. Our nanostrain and orientation reconstruction technique, depending only on molecular-level fibre symmetry, can be applied generally to determine the in situ dynamics of both natural and synthetic hierarchical nanocomposites.