Manganese oxides for catalytic combustion of VOCs are high profile owing to their excellent redox properties and oxygen storage capacities, while the precise regulation of microstructure to improve the activity remains challenging. Herein, imidazolium-based ionic liquids are employed as the template agents to synthesize a range of MnO2 for different structures and morphologies. The hydrogen bonding network of the ionic liquid and the π-π stacking interactions between the imidazole rings promoted the self-organization of [MnO6] into a specific structure. In this process, alteration of alkyl chain length of ionic liquids caused changes in surface tension and steric hindrance, affecting the growth of MnO2. A series of characterization results showed that MnO2 transformed from nanofibers to nanorods when the alkyl chain elongated from ethyl to octyl, accompanied by an increase in crystal size. This transformation decreased the specific surface area and surface-active oxygen of the catalyst, diminishing active sites available for the catalytic reaction. Therefore, the optimal catalytic performance of the prepared catalyst was achieved when the ionic liquid was selected as 1-ethyl-3-methylimidazolium tetrafluoroborate, with a propane conversion of 90% at 289 ºC. This work provided a feasible path to realize the microstructure engineering of non-noble metal catalysts.