Hard nutshells serve as natural models for lightweight yet exceptionally damage-resistant structures. Using microscopy and tomography, we investigated the hierarchical design of the pili nut (Canarium ovatum) across multiple length scales. Eight hierarchical levels (H0–H7) were distinguished, spanning organ, tissue, cellular, sub-cellular, and molecular level, with emphasis on the endocarp (H2–H6). The endocarp exhibits a multi-layered, “sandwich-like” organization (H3), with variation in layer morphology (H4) that potentially contributes to both strength and toughness. Unlike macadamia and Brazil nuts, the pili nut contains only a single vascular bundle, resulting in a less porous structure. Its macroscopically bipyramidal shape (H2) and absence of a suture line further suggest an inherent robustness. This study provides a first insight into the structural strategies underlying the mechanical resilience of the pili nut.