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A proportional relationship between the specific capacitance of MnO2 and the percentage of effective Mn centers that act as active sites in the Faradaic charge storage has been established on the basis of a tunnel structure–crystallization behavior correlation. A quantitative relationship between the effective Mn centers at the surfaces and in the tunnels can distinguish the specific capacitance values that arise from the adsorption/desorption and insertion/extraction processes, respectively, of different MnO2 crystallographic forms in the Faradaic charge storage. The different specific capacitance values between the MnO2 crystallographic forms are mainly attributed to the different effective utilizations of Mn centers in the size-limited tunnels. The present model demonstrates that increasing the percentage of effective Mn centers via decreasing the crystal size can facilitate obtaining MnO2-based electrode materials with higher specific capacitance values.