Nitrate-to-ammonia electroreduction (NO3RR) offers a sustainable alternative to the energy-extensive Haber–Bosch process. Previous studies have reported nitrogen-coordinated copper single-atom catalysts with impressive activity and selectivity. However, regulating the nitrogen coordination structure at the atomic scale and its impact on the catalytic mechanism are not yet clear. This work demonstrates a pyridinic-N-rich copper single-atom catalyst (PR-CuNC) derived from semi-interpenetrating polypyrrole-polyethyleneimine hydrogels for the NO3RR. By contrast to the catalyst with insufficient pyridinic nitrogen, PR-CuNC exhibits a maximum NH3 Faraday efficiency of 94.61 % and a yield rate of 130.71 mgNH3 mgCu−1 h−1 (3.74 mgNH3 h−1 cm−2). Theoretical evidence reveals that different N coordination types significantly affect the electronic structures of CuN4 sites, resulting in the enhanced intrinsic activity. Our results show that the nitrogen structure is highly relevant to the performance of NO3RR, underlining the importance of directly regulating the local coordination environment at the molecular level.