Abstract Aqueous zinc–ammonium hybrid batteries represent a promising direction for sustainable energy storage, yet their development is constrained by the limited understanding of multi‐ion synergistic mechanisms and the structural instability of conventional cathode materials. Herein, NH 4 + pre‐intercalated hexagonal WO 3 is proposed as a stable cathode and reveals a previously overlooked dual‐channel ion storage mechanism: surface Zn 2+ /NH 4 + co‐deposition and bulk H + /NH 4 + co‐intercalation. This synergistic process not only enhances specific capacity but also improves cycling stability by effectively mitigating structural stress and facilitating rapid ion transport. Through electrochromic visualization and density functional theory (DFT) calculations, it is demonstrated that H + / NH 4 + dominates insertion within the tunnels while Zn 2+ preferentially deposits on the surface. This work provides a new strategy for designing high‐performance multi‐ion energy storage systems through precise regulation of interfacial and bulk ion behaviors.