Walnut shell is lightweight material with high-strength and toughening characteristics, but it is different from other nut shells' microstructure with two or three short sclerotic cell layers and long bundle fibers. It is essential to explore the fracture resistance biomechanism of lightweight walnut shell and how to prevent damage of bionic structure. In this study, it is found that the asymmetric mass center and geometric center dissipated impact energy to the whole shell without loading concentration in the loading area. Diaphragma juglandis is a special structure improved walnut shell's toughening. The S-shape gradient porosity/elastic modulus distribution combined with pits on single auxetic sclerotic cells requires higher energy to crack expansion, then decreases its fracture behavior. These fantastic findings inspire to design fracture resistance devices including helmets, armor, automobile anti-collision beams, and re-entry capsule in spacecraft.