Transition metal@carbon heterostructures are an emerging material paradigm for enhancing Fenton-like catalysis, and the synthesis of this heterostructure with designed functionality derived from metal−organic frameworks (MOFs) is interesting and challenging. Herein, we developed MOF-on-MOF nanoarchitectures to construct a selectively functionalized nitrogen-doped cobalt@ carbon nanotube-grafted carbon (Co@NCNT/NC) polyhedron via the thermal treatment of elaborately designed ZIF-8@ZIF-67 core− shell precursors for water decontamination. Strikingly, the Co@ NCNT/NC heterojunction is more conducive to transporting electrons to adjacent Co atoms than Co@NC, because of its high d-band center, strong conductivity, and the formation of multiple C−Co bonds for electron tunneling. Deliberate material design and theoretical simulations unveil that the dual reaction centers in C−Co bonds significantly alter the electronic structure of Co atoms, which creates the electron-rich Co centers further enhancing the specific adsorption/activation of H 2 O 2 . Simultaneously, the loss of electrons in Co species reduces the surrounding energy levels, resulting in the electrons of pollutants adsorbed on the surface of Co@NCNT/NC entering Co species through C−Co chargetransfer bridges, thus maintaining the redox cycle of Co 2+ → Co 3+ → Co 2+ , and realizing the efficient and stable removal of pollutants. This work highlights the importance of the transition metal@carbon heterostructures to advanced catalytic oxidation and the MOF-on-MOF nanoarchitectures on nanomaterials synthetic chemistry.