Manganese (Mn)‐based aqueous zinc ion batteries show great promise for large‐scale energy storage due to their high capacity, environmental friendliness, and low cost. However, they suffer from the severe capacity decay associated with the dissolution of Mn from the cathode/electrolyte interface. In this study, theoretical modeling inspires that the amino acid molecule, isoleucine (Ile), can be an ideal surface coating material for α‐MnO2 to stabilize the surface Mn lattice and mitigate Mn dissolution, thereby enhancing cycling stability. Furthermore, the coated Ile molecular layers can accumulate Zn2+ ions from the electrolyte and promote those ions’ transport to the α‐MnO2 cathode while prohibiting H2O from accessing the α‐MnO2 surface, reducing the surface erosion. The compact organic–inorganic interface is experimentally synthesized for α‐MnO2 utilizing Ile that shows homogeneous distribution on the well‐defined Ile‐α‐MnO2 nanorod electrodes. The fabricated aqueous zinc‐ion battery exhibits a high specific capacity (332.8 mAh g−1 at 0.1 A g−1) and excellent cycling stability (85% after 2000 cycles at 1 A g−1) as well as good inhibition toward Mn2+ dissolution, surpassing most reported cathode materials. This organic–inorganic hybrid interface design provides a new, simple avenue for developing high‐performance and low‐cost Mn‐based aqueous zinc ion batteries (AZIBs).