The basic microstructure-dependent charge storage mechanisms of nanostructured MnO2 are investigated via dynamic observation of the growth and in situ probing the mechanical properties by using in situ AFM in conjunction with in situ nanoindentation. The progressive nucleation followed by three-dimensional growth yields pulsed current deposited porous nanostructured γ-MnO2, which exhibits a high specific capacitance of 437 F/g and a remarkable cycling performance with >96% capacitance retention after 10 000 cycles. The proton intercalation induced expansion of MnO2 can be self-accommodated by the localized compression and reduction of the porosity. More coincidentally, the proton intercalation induced softening is favorable for the elastic deformation of MnO2. This self-adaptive capability of nanostructured MnO2 could generate high structural reliability during cycling. These discoveries offer important mechanistic insights for the design of advanced electrochemical capacitors.