The pili nut (Canarium ovatum) exhibits exceptional mechanical resistance due to its unique hierarchical shell structure. Here we present our insights from investigations of the relationship between structure and mechanical properties where we combined morphological analyses, mechanical testing, and computational modeling. Our microscopic analysis revealed an eight-level hierarchical structure of the whole fruit, encompassing distinct levels: organ, tissue, cellular, and finally, molecular. At the tissue level of the endocarp, seven distinct layers, primarily composed of sclerenchymatous tissue, were identified. Tensile and compression tests on small samples revealed a Young’s Modulus of around 2800 MPa. Compression tests on whole and half nuts, coupled with digital image correlation (DIC) characterized the deformation behavior. Finite element (FE) simulations further elucidated the role of shell geometry in strain distribution and crack propagation. The findings highlight that circumferential strains perpendicular to the loading direction play a key role in initiating failure. Notably, the strategically oriented sclerenchymatous fibers arranged in distinct layers, exhibiting orthogonality to each other, effectively impeded crack propagation. This inherent anisotropy significantly contributes to the remarkable toughness of the nut, while the internal porosity facilitates a lightweight structure. By mimicking the distinctive architecture of nutshells, engineers can create composite structures with controlled failure mechanisms. These structures could combine the foam-like behavior of low-density materials with the strength and resilience of fibrous layers, enabling them to withstand high compression loads.