Manganese dioxide has received significant attention as a prospective cathode material in aqueous zinc-ion batteries (ZIBs) owing to its elevated working voltage and commendable energy density. Nevertheless, challenges such as structural instability, manganese dissolution, and poor electrical conductivity remain significant barriers to the practical application of research. Here, the MnO2 nanorods encapsulated in the amorphous carbon (MnO2@C) with core-shell structure are prepared by a special hard template method, and investigated as cathode materials for ZIBs. The amorphous carbon, characterized by its structural defects and disorder, manifests heightened active site density, thereby establishing an efficient conduit for charge transport. Concurrently, the nano-dimensional interstitial spaces augment the active sites available for zinc insertion reactions, thereby effectively curtailing the ion diffusion path and, consequently, engendering heightened electrochemical performance. Moreover, the distinctive core-shell architecture of MnO2@C not only furnishes substantial spatial accommodation but also serves to alleviate volume alterations throughout charge and discharge events. Consequently, MnO2@C demonstrates outstanding electrochemical performance, with reversible capacities of 210 mAh·g−1 and 50 mAh·g−1 at 0.1 A·g−1 and 1.6 A·g−1, respectively. Furthermore, even after 600 cycles at 0.8 A·g−1, it maintains exceptional cycling performance, reaching 102 mAh·g−1, endowing MnO2@C cathodes with robust competitiveness in aqueous ZIBs.