Copper-based catalysts are widely used in methanol steam reforming to produce hydrogen. In this paper, the supportive effect of the crystal phase of ZrO2 on Cu-based catalysts in methanol steam reforming is discussed. Monoclinic(m-), Tetragonal(t-) and mixed ZrO2 phases were prepared, and structure–activity relationships were investigated with XRD, H2-TPR, BET, HR-TEM and XPS. It was found that the catalyst with a 81.4% monoclinic ZrO2 crystal phase exhibited the highest methanol conversion (88.5%) and the highest hydrogen production rate (104.6 μmol/gcat·s) at 275 °C as it displayed the best reducing properties and more oxygen vacancies on the catalyst surface. Oxygen vacancies can produce more Cu1+ + Cu0, which is the active species for methanol steam reforming on the catalyst surface, and therefore affect catalytic activity.