Mitigating the mechanical degradation and enhancing the ionic/electronic conductivity are critical but challengeable issues toward improving electrochemical performance of conversion‐type anodes in rechargeable batteries. Herein, these challenges are addressed by constructing interconnected 3D hierarchically porous structure synergistic with Nb single atom modulation within a Co3O4 nanocage (3DH‐Co3O4@Nb). Such a hierarchical‐structure nanocage affords several fantastic merits such as rapid ion migration and enough inner space for alleviating volume variation induced by intragrain stress and optimized stability of the solid‐electrolyte interface. Particularly, experimental studies in combination with theoretical analysis verify that the introduction of Nb into the Co3O4 lattice not only improves the electron conductivity, but also accelerates the surface/near‐surface reactions defined as pesudocapacitance behavior. Dynamic behavior reveals that the ensemble design shows huge potential for fast and large lithium storage. These features endow 3DH‐Co3O4@Nb with remarkable battery performance, delivering ≈740 mA h g−1 after ultra‐long cycling of 1000 times under a high current density of 5 A g−1. Importantly, the assembled 3DH‐Co3O4@Nb//LiCoO2 pouch cell also presents a long‐lived cycle performance with only ≈0.059% capacity decay per cycle, inspiring the design of electrode materials from both the nanostructure and atomic level toward practical applications.