The byproducts of ammonia-selective catalytic reduction (NH3-SCR) process over MnFe/TiO2 catalysts under the conditions of both with and without SO2 poisoning were analyzed. In addition to the NH3-SCR reaction, the NH3 oxidation and the NO oxidation reactions were also evaluated at temperatures of 100–300 °C to clarify the reactions occurred during the SCR process. The results indicated that major byproducts for the NH3 oxidation and NO oxidation tests were N2O and NO2, respectively, and their concentrations increased as the reaction temperature increased. For the NH3-SCR test without the presence of SO2, it revealed that N2O was majorly from the NH3-SCR reaction instead of from NH3 oxidation reaction. The byproducts of N2O and NO2 for the NH3-SCR reaction also increased after increasing the reaction temperature, which caused the decreasing of N2-selectivity and NO consumption. For the NH3-SCR test with SO2 at 150 °C, there were two decay stages during SO2 poisoning. The first decay was due to a certain amount of NH3 preferably reacted with SO2 instead of with NO or O2. Then the catalysts were accumulated with metal sulfates and ammonium salts, which caused the second decay of NO conversion. The effluent N2O increased as poisoning time increased, which was majorly from oxidation of unreacted NH3. On the other hand, for the NH3-SCR test with SO2 at 300 °C, the NO conversion was not decreased after increasing the poisoning time, but the N2O byproduct concentration was high. However, the SO2 led to the formation of metal sulfates, which might inhibit NO oxidation reactions and cause the concentration of N2O gradually decreased as well as the N2-selectivity increased.