The modification of axial ligands (ALs) can greatly affect the electrocatalytic performance of M-N-C single-atom catalysts (SACs), whereas their potential ligand-active site interaction mechanism is still elusive. Herein, an asymmetric MnN3H2 substrate model with nitrogen vacancies was constructed based on density functional theory, and 21 different types of ALs were introduced to construct MnN3H2-X (X = F, Cl, Br, I, P, S, O, H, OH, OOH, HCO3, HSO4, NO, NO2, NH, NH2, NH3, CH, CH2, CH3, C6H5) SACs. Formation and binding energy calculations were utilized to screen thermodynamically stable structures, followed by calculations of their free energy variations and overpotentials for the OER/ORR. The results show that MnN3H2-NO (0.49 V for OER) and MnN3H2-P (0.38 V for ORR) demonstrate outstanding electrocatalytic performance due to their lower overpotentials, which are conform to the volcano plot analysis. Moreover, MnN3H2-P (1.17 V) and MnN3H2-CH (1.20 V) have favorable bifunctional catalytic properties. The remarkable electrocatalytic activity originates from the synergistic regulation of ALs and Mn, thereby optimizing the charge redistribution and adsorption of intermediates, ultimately improving the subsequent ORR and OER. This study establishes theoretical underpinnings and mentality of designing for the directional devisal of highly active Mn-N-C SAC electrocatalysts.