Manganese dioxide/multiwalled carbon nanotubes (MnO2/MWCNTs) were synthesized by chemically depositing MnO2 onto the surface of MWCNTs wrapped with poly(sodium-p-styrenesulfonate). Then, polyaniline (PANI) with good supercapacitive performance was further coated onto the MnO2/MWCNTs composite to form PANI/MnO2/MWCNTs organic–inorganic hybrid nanoarchitecture. Electrochemical performance of the hybrid in Na2SO4–H2SO4 mixed acidic electrolytes was evaluated by cyclic voltammetry (CV) and chronopotentiometry (CP) in detail. Comparative electrochemical tests revealed that the hybrid nanoarchitecture could operate in the acidic medium due to the protective modification of PANI coating layer onto the MnO2/MWCNTs composite, and that its electrochemical behavior was greatly dependent upon the concentration of protons in the acidic electrolytes. Here, PANI not only served as a physical barrier to restrain the underlying MnO2/MWCNTs composite from reductive-dissolution process so as to make the novel ternary hybrid material work in acidic medium to enhance the utilization of manganese oxide as much as possible, but also was another electroactive material for energy storage in the acidic mixed electrolytes. It was due to the existence of PNAI layer that an even larger specific capacitance (SC) of 384Fg−1 and a much better SC retention of 79.9% over 1000 continuous charge/discharge cycles than those for the MnO2/MWCNTs nanocomposite were delivered for the hybrid in the optimum 0.5M Na2SO4–0.5M H2SO4 mixed acidic electrolyte.