<p>Single-atom catalysts (SACs) are favored owing to their well-defined motifs and notable CO selectivity in electrochemical CO₂ reduction. However, the dynamic coordination evolution under working conditions and the structure-activity relationships remain highly puzzling. Herein, we suggest that flexible Zn–P₃ nanodomains with weak-bond interactions may exhibit a potential-dependent structural modulation under working conditions compared to Zn–N₄ configurations. A possible metastable state with reduced Zn–P_x-like coordination may be formed from the Zn–P₃ structure under CO₂ reduction working conditions. Based on in situ spectroscopy analysis, deuterium isotope kinetic analysis, and theoretical calculations, the low-coordination Zn and the possibly perturbed P sites may serve as efficient active sites for the first step of sequential proton–electron transfer in the CO₂ electroreduction. The collaborative assignments within this dynamic catalytic nanodomain, rather than at individual metal site, may contribute to the improved the intrinsic activity, which delivers a high turnover frequency (47,690 h⁻¹) and a CO production rate (213 mL h⁻¹ cm⁻²) at 500 mA cm⁻² for 100 h. Our work elucidates the dynamic coordination-governed mechanisms of SACs and underscores the necessity of probing their structural basis under operating conditions.</p>