Understanding of surface defects of a catalyst during the reaction process is critical to establish an accurate structure‐activity relationship. Herein, combining operando X‐ray diffraction/ photoelectron spectroscopy with scanning probe microscope, we have firstly established the correlations between CO2 photoreduction activities and crystal‐structure/active‐site of defective ZnAl layered double hydroxides (ZnAl‐LDH). Specifically, the introduction of oxygen vacancies in ZnAl‐LDH could effectively promote the selective adsorption of both CO2 and H2O molecules on surface Al and Zn active sites, respectively, leading to opposite transition states and the evident shrinking of crystalline structures. Upon light irradiation, the adsorbed CO2 molecules transformed into *COOH intermediate on surface Al active sites, while the H2O molecules dissociated into OH group on Zn sites to provide proton, simultaneously leading to the expansion of crystalline structures and increase of layer spacing. Accordingly, these defect‐dependent evolutions of surface active sites and crystalline structure contributed to the significant improvement of CO2 reduction to CO activity (17.2 μmol g‐1 h‐1), much higher than that of pristine ZnAl‐LDH (6.3 μmol g‐1 h‐1). This work provides new insights for in‐depth understanding of the electronic and crystalline changes of defective photocatalysts during the reaction process.