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The electrochemical conversion of nitrate pollutants into value‐added ammonia is a feasible way to achieve artificial nitrogen cycle. However, the development of electrocatalytic nitrate‐to‐ammonia reduction reaction (NO3−RR) has been hampered by high overpotential and low Faradaic efficiency. Here we develop an iron single‐atom catalyst coordinated with nitrogen and phosphorus on hollow carbon polyhedron (denoted as Fe−N/P−C) as a NO3−RR electrocatalyst. Owing to the tuning effect of phosphorus atoms on breaking local charge symmetry of the single‐Fe‐atom catalyst, it facilitates the adsorption of nitrate ions and enrichment of some key reaction intermediates during the NO3−RR process. The Fe−N/P−C catalyst exhibits 90.3 % ammonia Faradaic efficiency with a yield rate of 17980 μg h−1 mgcat−1, greatly outperforming the reported Fe‐based catalysts. Furthermore, operando SR‐FTIR spectroscopy measurements reveal the reaction pathway based on key intermediates observed under different applied potentials and reaction durations. Density functional theory calculations demonstrate that the optimized free energy of NO3−RR intermediates is ascribed to the asymmetric atomic interface configuration, which achieves the optimal electron density distribution. This work demonstrates the critical role of atomic‐level precision modulation by heteroatom doping for the NO3−RR, providing an effective strategy for improving the catalytic performance of single atom catalysts in different electrochemical reactions. [ABSTRACT FROM AUTHOR]