Among multitudinous metal-oxide catalysts for the selective catalytic reduction of NOx with NH3 (NH3-SCR), Mn-based catalysts have become very popular and developed rapidly in recent years because of its superior low-temperature denitrification activity, mainly originating from multi-valence of Mn. Most studies suggest that the catalytic activity of multi-component oxides is superior to that of single-component catalysts owing to the synergistic effect among the metallic elements in such materials, of which more attentions have been given to Ce as an additive owing to its powerful oxygen storage capacity, redox ability and its ready availability. As the core of SCR technology, the research points in catalyst development at the present stage of all researchers in countries mainly centralize on the optimization of active components, carriers, calcination temperature, calcination time and temperature-raising procedure, giving little thought to the effects of the calcination atmosphere. In the present work, Ce-modified Mn-based catalysts were prepared by a simple impregnation method. The effects of the calcination atmosphere (N2, air or O2) on the performance of the resulting materials during NH3-SCR and its causes of the differences were subsequently investigated and characterized using various analytical methods. Data obtained from X-ray diffraction, thermogravimetry and temperature-programmed reduction with hydrogen show that calcination under N2 reduces both the degree of oxidation and crystallization of the MnOx. Scanning electron microscopy also demonstrates that the use of N2 inhibits the growth of grains and increases the dispersion of the catalysts. In addition, the results of temperature-programmed desorption with ammonia indicate that catalysts calcined under N2 exhibit a greater quantity of acid sites. Finally, X-ray photoelectron spectrometry and activity results demonstrate that MnOx in the lower valence states is more favorable for NH3-SCR reactions. In conclusion, catalysts calcined under N2 show superior performance during NH3-SCR for NOx removal, allowing NO conversions up to 94% at 473 K.