Granular materials, composed of densely packed particles, are known to possess unique mechanical properties that are highly dependent on the surface structure of the particles. A microscopic understanding of the structure‐property relationship in these systems remains unclear. Here, supra‐nanoparticle clusters (SNPCs) with precise structures are developed as model systems to elucidate the unexpected elastic behaviors. SNPCs are prepared by coordination‐driven assembly of polyhedral oligomeric silsesquioxane (POSS) with metal‐organic polyhedron (MOP). Due to the disparity in sizes, the POSS‐MOP assemblies, like their classic nanoparticles counterparts, ordering is suppressed, and the POSS‐MOP mixtures will vitrify or jam as a function of decreasing temperature. An unexpected elasticity is observed for the SNPC assemblies with a high modulus that is maintained at temperatures far beyond the glass transition temperature. From studies on the dynamics of the hierarchical structures of SNPCs and molecular dynamic simulation, the elasticity has its origins in the interpenetration of POSS‐ended arms. The physical molecular interpenetration and inter‐locking phenomenon favors the convenient solution or pressing processing of the novel cluster‐based elastomers. Supra‐nanoparticle clusters (SNPCs) were synthesized by convergence of metal–organic polyhedron scaffolds with precise giant building blocks. The mechanical properties and structural dynamics can be regulated by fine‐tuning the surface functionalization of the terminal POSS moieties. Unexpected elasticity with high Young's modulus of the OPOSS‐ended SNPCs was found to be highly correlated with the interpenetration of the neighboring GLs.