Understanding the atomic and electronic changes of active sites promotes the whole new sight into electrochemical carbon dioxide reduction reaction (CO₂RR), which provides a feasible strategy to achieve carbon neutrality. Here we employ operando high-energy resolution fluorescence-detected X-ray absorption spectroscopy (HERFD-XAS) to track the structural evolution of Ni(II) phthalocyanine (NiPc), considered as the model catalysts with uniform Ni-N₄-C₈ moiety, during the CO₂RR. The HERFD-XAS method is in favor of elucidating the interaction of the reactant/catalyst interface from the atomic electronic structure dimension, facilitating the establishment of the catalytic mechanism and the dynamic structure changes. Based on operando measurement, surface sensitive difference spectra (∆µ) and spectroscopy simulation, the interfacial interactions between the active sites of NiPc and reactants are monitored and the Ni species gradually reduced by increasing the applied potential is discovered. HERFD-XAS method offers an advanced and powerful tool for elucidating the complex catalytic mechanism in further various systems.