Understanding the mechanisms and manipulations of atomic hydrogen during electrocatalytic hydrogen atom transfer (HAT) is critical for achieving the selective reduction of nitrate to ammonia. However, the molecular action of HAT in the reaction of nitrate-to-ammonia conversion remains poorly understood, particularly given the complexity of 8-electron transfer process and the kinetics of different hydrogen species (e.g., adsorbed Hads and free •H radical). Herein, we develop a trace ruthenium anchored self-supported heterostructure (Ru-Ni2P/NF), in which Ni2P accelerates water dissociation to generate hydrogen intermediates and Ru optimizes Hads stabilization. Experimental results indicate 97.5% nitrate conversion with 86.4% NH3 selectivity within 4 h. Furthermore, H-species kinetic analysis and H/D isotopic labeling demonstrate a difference in Hads and •H functionalities; Hads dominates nitrite reduction with a 14.6-fold higher rate constant than •H-mediated pathways. DFT calculations identify Ru-induced symmetry breaking in nitrate (N-O bond elongation: 0.039 Å) as the critical activation step, and a complete deoxygenation-hydrogenation mechanism (*NO3- → *N → *NHx intermediates) is validated by in situ FTIR and Gibbs free energy profiles. Notably, the reduction of nitrite by Ru-Hads is thermodynamically favored without additional potential, which is consistent with the high rate of Hads reduction of nitrite to ammonia in the experiment. This study generates valuable insights into HAT-mediated nitrate conversion at a molecular level, providing a blueprint for catalytic systems in environmental remediation and green ammonia synthesis.