An in situ measurement of a CO2 reduction reaction (CO2RR) in Cu-phthalocyanine (CuPC) molecules adsorbed on an Au(111) surface is performed using electrochemical scanning tunneling microscopy. One intriguing phenomenon monitored in situ during CO2RR is that a well-ordered CuPC adlayer is formed into an unsuspected nanocluster via molecular restructuring. At an electrode potential of -0.7 V versus Ag/AgCl, the Au surface is covered mainly with the clusters, showing restructuring-induced CO2RR catalytic activity. Using a measurement of X-ray photoelectron spectroscopy, it is revealed that the nanocluster represents a Cu complex with its formation mechanism. This work provides an in situ observation of the restructuring of the electrocatalyst to understand the surface-reactive correlations and suggests the CO2RR catalyst works at a relatively low potential using the CuPC-derived Cu nanoclusters as active species.