Cu-ZnO-Al2O3 catalysts are used as the industrial catalysts for water gas shift (WGS) and CO hydrogenation to methanol reactions. Herein, via a comprehensive experimental and theoretical calculation study of a series of ZnO/Cu nanocrystals inverse catalysts with well-defined Cu structures, we report that the Cu-ZnO catalysts undergo Cu structure-dependent and reaction-sensitive in situ restructuring during WGS and CO hydrogenation reactions under typical reaction conditions, forming the active sites of CuCu(100)-hydroxylated ZnO ensemble and CuCu(611)Zn alloy, respectively. These results conclude the long-existing debates and provide the feasible guideline for optimizing the structures of Cu-ZnO-Al2O3 catalysts.