Organic compounds are promising cathode materials for efficient aqueous Zn-ion batteries due to their structural diversity and tunability, but their limited capacity and inadequate cycle life plague the practical applications. In this study, a two-step MOF-derived pyrolysis and oxidative polymerization strategy has been developed to prepare locally protonated nitrogen-doped carbon dodecahedron@polyaniline (NCD@PANI) nanohybrids as an efficient cathode for ultra-stable Zn-ion storage. The N-doped carbon skeleton with rich pyrrolic-N groups can serve as the coordinator to regulate the local protonation environment of PANI through strong hydrogen bond interactions, thus promoting the redox reactions. As expected, the as-assembled NCD@PANI//Zn battery exhibits excellent electrochemical performances, including a high capacity of 325 mAh g−1 at 0.2 A g−1 and a long cycle life of 5000 cycles. The governing Zn2+/H+ dual-ion insertion/extraction mechanism is further unveiled using a series of ex situ measurements. This work provides a new strategy to develop high-performance organic compound electrodes for efficient energy storage devices through the technique of local protonation.