The effects of SO2 and H2O on the low-temperature selective catalytic reduction (SCR) activity over MnOx/ZrO2/MWCNTs and MnOx/ZrO2/MWCNTs catalysts modified by Ce or Y was studied. MnCeZr and MnYZr catalysts reached nearly 100% and 93.9% NOx conversions at 200 °C and 240 °C, respectively. They displayed a better SO2 tolerance, and the effect of H2O was negligible. The structural properties of the catalysts were characterized by XRD, H2-TPR, XPS, and FTIR before and after the reaction. The results showed that Ce could increase the mobility of the oxygen and improve the valence and the oxidizability of manganese, while the effect of Y was the opposite. This might be the main reason why the catalytic activity of MnCeZr was better than MnYZr in the presence or absence of SO2 and H2O. Doping Ce or Y broadened the active temperature window. Ce or Y, which existed in the catalysts with a high dispersion or at the amorphous state, preferred to react with SO2 to form sulfate species, and protected the manganese active sites from combing with SO2 to some extent, which coincided with the theory of ionic polarization.