Mn-Ce/CeAPSO-34 was prepared, in which manganese and cerium were supported on the surface through using the Ethanol dispersion method, while cerium was incorporated in the SAPO-34 framework by a one-step hydrothermal method. Based on our previous study, a strong synergistic effect of cerium presented in the framework and the surface was existing in Mn-Ce/CeAPSO-34 catalyst, which showed outstanding SO2 tolerance and H2O resistance in the low-temperature NH3-SCR. In situ FT-IR and DFT calculations were used to investigate the synergistic effects. Based on the characterization results of in situ FT-IR study, it was found that more amount of nitrate species and NH3 species adsorbed on the surface of Mn-Ce/CeAPSO-34, while less the amount of sulfate species deposited during reaction process, which in the presence of SO2. Meanwhile, DFT calculations revealed that Ce site supported on the surface, which neighbored by Ce site in the framework more were capable of reacting with NO and NH3.