Two manganese oxides with the same nanorod-shaped morphology but different crystal structures, tunnel and layer structures, were synthesized and investigated for selective catalytic reduction of NOx with NH3 (NH3-SCR) at low temperature. Tunneled alpha-MnO2 had much higher catalytic activity than layered delta-MnO2 under the same reaction conditions. Experiment results revealed that the surface area was not the main factor to affect the NH3-SCR activities over the MnO2 nanorods and that the activities were structure sensitive. Structure analysis and temperature-programmed desorption experiments of NH3 (NH3-TPD) suggested that the exposed (110) plane of alpha-MnO2 had many Mn cations in coordinatively unsaturated environment, while all of the Mn cations on the exposed (001) plane of delta-MnO2 were in coordinatively saturated environment. Thus, alpha-MnO2 possessed many more Lewis acid sites. Furthermore, alpha-MnO2 has weaker Mn - O bonds and an efficient tunnel structure, which are favorable characteristics for NH3 adsorption. Moreover, X-ray photoelectron spectroscopy (XPS) and thermal gravimetric (TG) analysis indicated that alpha-MnO2 obtained a higher capability for NH3 and NOx activation than delta-MnO2. The crystal structure and surface properties of alpha-MnO2 are more suitable to the adsorption of NH3 and activation of NH3 and NOx, which accounts for the higher catalytic activity of the alpha-MnO2 nanorods.