Mesoporous MnO2 with uniform nanorod morphology and mesoporous β-MnO2 were prepared using SBA-15 and KIT-6 as the templates, respectively. XRD, nitrogen adsorption analysis, SEM, TEM and EDX techniques were used for the structural characterization. The electrochemical properties of the MnO2 samples were studied using alkaline Zn/MnO2 batteries in a 9M KOH electrolyte solution. Compared to the commercial electrolytic manganese dioxide (EMD), the discharge capacity of the mesoporous MnO2 nanorods increased by 74.98%, 119.74% and 146.19% at constant currents of 50, 250 and 500mAg−1, respectively, while the discharge capacity of the mesoporous β-MnO2 increased by 63.58%, 95.14% and 100.23%.