Methane selective catalytic reduction (CH4-SCR) technology has shown promise for controlling NOx emissions from natural gas generator sets. This study presents a highly efficient Ce30In15/HBEA catalyst featuring dual active sites, Al-O–(InO+)-Si site for CH4 activation and ceria oxygen vacancy (Ce3+-□) site for NOx activation. However, the CH4-SCR activity of this catalyst decreased in the presence of H2O, SO2, C3H6, and CO2. The inhibitory effects on CH4-SCR activity followed by the sequence: H2O > SO2 > C3H6 > CO2. In particular, H2O combined with Al-O–(InO+)-Si to form inactive In(OH)3-zz+ species and occupied Ce3+-□, preventing Ce4+-NO3–/NO2– formation. In/Ce sulfate formation via the reaction between SO2 and In/Ce active sites hindered CH4 and NOx adsorption and activation. The formed carbon deposits covered the active sites on the catalyst surface due to incomplete C3H6 oxidation. In comparison, the dual active sites were almost unaffected by CO2. Overall, this study provides a basis for the rational design of novel catalysts for CH4-SCR.