We synthesized Cu single atoms embedded in a N-doped porous carbon catalyst with a high Faradaic efficiency of 93.5% at −0.50 V (vs. RHE) for CO₂ reduction to CO. The evolution of Cu single-atom sites to nanoclusters of about 1 nm was observed after CO₂ reduction at a potential lower than −0.30 V (vs. RHE). The DFT calculation indicates that Cu nanoclusters improve the CO₂ activation and the adsorption of intermediate *COOH, thus exhibiting higher catalytic activity than CuN_x sites. The structural instability observed in this study helps in understanding the actual active sites of Cu single atom catalysts for CO₂ reduction.