Cu-modified SO42−/ZrO2 catalysts (XCu-SZ) with different Cu loading contents were prepared by sulfation of ZrOCl2·8H2O with (NH4)2SO4 to form SO42−/ZrO2 (SZ) followed by impregnation of SZ with a Cu precursor. The resulting XCu-SZ catalysts combined with a CuO–ZnO–ZrO2 catalyst were tested for CO2 hydrogenation to dimethyl ether (DME). The results indicated that the unmodified SZ catalyst exhibited the maximum DME yield (3.7%) which was 2.0–2.6 times higher than the DME yield of all XCu-SZ catalysts at the beginning of reaction. However, the DME yield over the unmodified SZ catalyst rapidly decreased, while that of all XCu-SZ catalysts gradually increased during the time-on-stream experiment. After 100 h, the 6 wt% Cu-modified SZ catalyst achieved the maximum DME yield of 3.2% at 260 °C and 20 bar, while the DME yield of the unmodified SZ catalyst was only 2.5%. The NH3-TPD and XPS analyses indicated that more strong acid sites were present on the unmodified SZ catalyst, resulting in a coke formation and thus the rapid deactivation. For the XCu-SZ catalysts, Cu0 was formed on the surface of SZ after the reduction with H2 which accounted for the active site of hydrogenolysis of methanol to methane. During the time-on-stream experiment, Cu0 was progressively transformed to Cu2S through poisoning, leading to the continued increase of DME yield.