Electrocatalytic nitrate reduction reaction (e-NO3RR) offers a promising alternative method for nitrogen cycling and ammonia (NH3) production under ambient conditions. However, the method is still in the dilemma of lowering the reaction overpotential and increasing the reaction activity. We successfully developed the composition-adjustable Co6Mo6C/Co/N-doped carbon (NC) catalysts by in situ carbonization of Co-based metal-organic framework (MOF) with the constrained phosphomolybdic acid. After adjusting the ratio of Co0 and Co6Mo6C, Co6Mo6C/Co/NC-3 could satisfy both NO3− conversion at low potential and NHx hydrogenation, and synthesize ammonia efficiently through the synergistic effect of Co0 and Co6Mo6C. It achieved an ammonia yield rate as 1233.2 µg·h−1·mgcat−1 and Faradaic efficiency of NH4+ 93.6% at −0.33 V vs. reversible hydrogen electrode (RHE). Importantly, density functional theory (DFT) calculations and experimental results have demonstrated for the first time the excellent adsorption of nitrite (NO2−) by the Mo sites of Co6Mo6C during e-NO3RR, avoiding the undesirable accumulation of NO2−.