Electrochemical carbon dioxide reduction reaction (CO₂RR) into high-value added chemicals and fuels has aroused wide attention, but suffers from high overpotential and poor selectivity. Herein, nitrogen-doped carbon supported Fe and Mn heteronuclear single atom catalysts with different Fe and Mn inter-site distance were fabricated via a templating isolation approach and tested for CO₂RR to CO in an aqueous solution. The catalyst with atomically dispersed Fe and Mn sites in close proximity exhibited the highest CO₂RR performance, with a CO Faradaic efficiency of 96% at a low overpotential of 320 mV, and a Tafel slope of only 62 mV·dec⁻¹, comparable to state-of-the-art gold catalysts. Experimental analysis combined with theory highlighted that single Mn atom at the neighboring site of Fe enhanced the electronic localization of Fe center, which facilitated the generation of key *COOH intermediate as well as CO* desorption on Fe, leading to superior CO₂RR performance at low overpotentials. This work offers atomic-level insights into the correlation between the inter-site distance of atomic sites and CO₂RR performance, and paves a new avenue for precise control of single-atom sites on carbon surface for highly active and selective electrocatalysts.