Due to the high specific surface area, abundant nitrogen and micropores, ZIF-8 is a commonly used precursor for preparing high performance Fe-N-C catalysts. However, the Zn element is inevitably remained in the prepared Fe-N-C catalyst. Whether the residual Zn element affects the catalytic activity and active site center of the Fe-N-C catalyst caused widespread curiosity, but has not been studied yet. Herein, we built several Fe, Zn, and N co-doped graphene models to investigate the effect of Zn atoms on the electrocatalytic performance of Fe-N-C catalysts by using density functional theory method. The calculation results show that all the calculated Fe-Zn-Nx structures are thermodynamically stable due to the negative formation energies and relative stabilities. The active sites around Fe and Zn atoms in the structure of Fe-Zn-N6(III) show the lowest oxygen reduction reaction (ORR) and oxygen evolution reaction (OER) overpotentials of 0.38 and 0.43 V, respectively. The bridge site of Fe-Zn in Fe-Zn-N5 shows the lowest η HER of −0.26 V. A few structures with a better activity than that of FeN4 or ZnN4 are attributed to the synergistic effects between Fe and Zn atoms. The calculated ORR reaction pathways on Fe-Zn-N6(III) show that H2O is the final product and the ORR mechanism on the catalyst would be a four-electron process, and the existence of Zn element in the Fe-N-C catalysts plays a key role in reducing the ORR activation energy barrier. The results are helpful for the deep understand of high-performance Fe-N-C catalysts.