In2O3/Co3O4 catalysts with various crystal structure of In2O3 were successfully prepared by means of regulating the amount of citric acid, and were applied for CO2 hydrogenation to methanol to understand the structure-activity relationship. With the increase of citric acid content in the impregnation process, hexagonal In2O3 (h-In2O3) is gradually transformed into cubic In2O3 (c-In2O3). The interaction and electron transfer between c-In2O3 and Co3O4 are stronger than those between h-In2O3 and Co3O4. In the In2O3/Co3O4 catalysts prepared with citric acid, phase transformations were observed under reaction conditions of 4 MPa and 300 °C. Initially, h-In2O3 transitions into c-In2O3. Concurrently, there is a transformation of In2O3 and Co3O4 into metallic cobalt (Co0) and the compound Co3InC0.75. Except for h-In2O3/Co3O4 containing mixed h-In2O3 and c-In2O3, In2O3 in all other catalysts exists in the form of c-In2O3. Owing to stronger interaction between c-In2O3 and Co0, dissociated hydrogen atoms diffuse more easily from the metallic Co0 to c-In2O3 to produce more oxygen vacancies, accompanied with the formation of more inactive Co3InC0.75 (70 wt% for c-In2O3/Co3O4 vs 58 wt% for h-In2O3/Co3O4). However, h-In2O3/Co3O4 has stronger adsorption ability of CO to improve methanol selectivity. Thus, it can be observed that the CO2 conversion and methanol selectivity of the catalyst are directly related to the In2O3 crystal phase for In2O3/Co3O4 catalysts. To be specific, h-In2O3/Co3O4 has the higher selectivity of methanol, while c-In2O3/Co3O4 exhibits the higher conversion of CO2 and methanol space-time yield.