Engineering single-atom electrocatalysts (SACs) of geometries and electronic structures at atomic level to overcome the critical trade-off in catalytic performance remains a significant challenge. Here, we report a novel metal–nonmetal pair sites with non-bonding interaction to achieve dual enhancements of activity and selectivity for nitrogen reduction reaction (NRR). The stable non-bonding structure of W-Se atom pairs on C3N4 support (W-SeC3N4) was engineered by photo-assisted cryogenic reduction. Distal Se-atom coupling drives a fine-tuning of surface-localized electronic state on center W-atom through genuine chemical interaction and modulates the adsorption energies of intermediates like *NNH, *NH and *NH2. W-SeC3N4 thus demonstrates a NH3 yield rate of 74.6 ug h−1 mgcat−1 and >38.2 % selectivity, surpassing all current non-precious metal SACs. Our work supplies an advanced strategy for the rational design of SACs in complex chemical reactions involving multi-step intermediates.