Electrocatalytically driven reduction of nitrate (NO3−) from NO3−-laden wastewater to ammonia (NH3) has emerged as a promising complementary strategy to the energy-intensive Haber-Bosch process. Herein, based on density functional theory (DFT) calculations, 14 organic ionic groups are found to significantly improve the electrocatalytic reduction of NO3− to NH3 (eNO3RR-to-NH3) activity of typical M−N4−C (M = Fe, Co, and Ni) catalysts by axially ligating metal center, among which Ethyl thiolate axially ligated Co−N4−C exhibits the highest eNO3RR-to-NH3 activity with the limiting potential (UL) of -0.11 V. 4-Mercaptobenzoic acid and Thiophenolate axially ligated Fe−N4−C can inhibit the NN coupling reaction while having high eNO3RR-to-NH3 activity (UL = -0.16, -0.31 V, respectively) and thus have better NH3 selectivity. Furthermore, ΔGH*NO and ICOHP (integrated crystal orbital hamilton populations) between the 3d orbital of M and 2p orbital of N (*NO) atoms show remarkable volcano relationship for L−Fe−N4−C systems and linear relationship with R-Square of 0.83 occurs for L−Co−N4−C systems. There is an excellent linear relationship (R-Square is 0.88) between ICOHP and UL for the L−Co−N4−C systems. Hence, the ICOHP can work as an excellent thermodynamic activity descriptor for eNO3RR-to-NH3 over L−Co−N4−C catalysts. The three catalysts are concluded to be promising electrocatalysts for eNO3RR-to-NH3.