Aqueous zinc ion secondary batteries (ZIBs) have recently attracted considerable attention and global interest due to their low cost, aqueous-based nature and great safety. Unfortunately, the intrinsic properties of poor cycle life, low energy density and uncontrolled dendrite growth during the charge/discharge process for metallic Zn anodes significantly hinder their practical application. In this work, we rationally designed two-dimensional (2D) δ-MnO₂ nanofluidic channels by the ordered restacking of exfoliated MnO₂ single atomic layers, which exhibited a high zinc ion transport coefficient (1.93 × 10⁻¹⁴ cm² s⁻¹) owing to their appropriate d-spacing and the negative charge of the inner channel walls. More importantly, we found that Zn dendrite growth was prevented in the as-assembled ZIBs, resulting in superior stability compared with the bulk-MnO₂ sample. Our design sheds light on developing high-performance ZIBs from two-dimensional nanofluidic channels, and this strategy might be applicable to the storage of other metal ions (Mg²⁺, Ca²⁺, Al³⁺, etc.) in next-generation electrochemical energy storage devices.