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The rational control of the active site of metal-organic frameworks (MOFs) derived nanomaterials is essential to build efficient bifunctional oxygen reduction/evolution reaction (ORR/OER) catalysts. Accordingly, through designing and constructing a Co3O4-Co heterostructure embedded in Co, N co-doped carbon polyhedra derived (Co3O4-Co@NC) from the in-situ compositions of ZIF-67 and cobalt nanocrystals synthesized by the strategy of in-situ NaBH4 reduction, the dual-active site (Co3O4-Co and Co-Nx) is synchronously realized in a MOFs derived nanomaterials. The formed Co3O4-Co@NC shows excellent bifunctional electrocatalytic activity with ultra-small potential gap (ΔE = Ej=10 (OER) - E1/2 (ORR)) of 0.72 V, which surpasses the commercial Pt/C and RuO2 catalysts. The theory calculation results reveal that the excellent bifunctional electrocatalytic activity can be attributed to the charge redistribution of Co of Co-Nx induced by the synergistic effects of well-tuned active sites of Co3O4-Co nanoparticle and Co-Nx, thus optimizing the rate-determining step of the desorption of O2* intermediate in ORR and OH* intermediate in OER. The rechargeable Zn-air batteries with our bifunctional catalysts exhibit superior performance as well as high cycling stability. This simple-effective optimization strategy offers prospects for tuning the active site of MOF derived bifunctional catalyst in electrochemical energy devices.