Herein, a robust MOFs-derived super-carbon embedding with single atom Co/Ni anode materials for LIBs is developed by one-step annealing of the core–shell precursor ZIF-8@ZIF-67 with the introduction of dimethylglyoxime nickel as Ni source. The characterization results clearly indicate that atomic Co/Ni active sites accompanied with suitable CoNi nanoparticles are evenly embedded in the MOF-derived hollow rich-nitrogen carbon matrix. Simultaneously, moderate short carbon nanotubes root in polyhedral surface under the catalytic effect from the CoNi nanoparticles and construct an advanced conductive network. As a result, it delivers a high reversible lithium-ion storage capacity of 462.1 mAh g⁻¹ at a current density of 0.5 A g⁻¹ over 500 cycles, excellent rate performance of 223.28 mAh g⁻¹ even at a high current density of 2 A g⁻¹, which is much higher than most of reported carbon-based electrode materials. The enhanced lithium storage performance mainly derives from the moderate affinity of the Li by the atomic Co/Ni active sites incorporated with their powerful catalytic effect assisting MOF-derived rich-N doped carbon base. Moreover, the superior nano-structure of the hollow rich-nitrogen carbon skeleton with in-situ grown short carbon nanotubes improves the conductivity of electrode materials, relieves the volume expansion and accelerates the migration rate of lithium ions and electrons. The theoretical calculation further confirms the superior affinity of the Li on atomic Co/Ni active sties.