Overconsumption of fossil energy has increased the CO₂ concentration in the atmosphere, leading to severe climatic problems. Toward establishing a sustainable energy system, it is desirable to develop carbon-neutral fuels, for which a promising approach is electrochemical conversion of CO₂ to useful products powered by electricity generated from renewable energy sources. However, due to slow kinetics and diverging reaction of electrochemical CO₂ reduction, high-performance catalysts are required. In this work, we have designed three copper (Cu)-complexes and one of them (CuPc) have exhibited high efficiency and selectivity for electrochemical reduction of CO₂ to methane. Using in situ X-ray absorption spectroscopy we find CuPc undergoes reversible structural and oxidation state changes to form nanometer size Cu metallic clusters, while the other two decompose irreversibly. With the help from density functional theory, the small but stable Cu clusters generated in situ during reaction is identified as the reaction active site of electrochemical CO₂ reduction and is responsible for CuPc’s high efficiency and selectivity. The insights learned from this study provide new ways to control the catalytic site at molecule level for the development of high electrocatalytic nano-materials.