Structural hierarchy plays an important role in the mechanical properties of natural materials. In this work, the concept of hierarchy was applied to topological interlocking assemblies to integrate different toughening strategies of multiple biologicals. Multi-material additive manufacturing was adopted to fabricate the bio-inspired interlocking structures comprised of discrete hard building blocks and soft intricate interfaces. An approach combining finite element simulation with direct mechanical testing on 3D-printed samples was conducted to investigate the mechanical consequences of these samples. It was found that the introduction of hierarchical surface design enabled the original interlocking assemblies to own additional interlocking effects at a smaller length scale, resulting in increased strength, stiffness, and toughness by 42.4%, 31.2%, and 83.8%, respectively.