MnO2 is a promising cathode material for aqueous zinc-ion batteries (AZIBs) with potential applications in large-scale energy storage systems. However, its practical use is hindered by poor cyclic stability and slow diffusion kinetics. Despite considerable efforts, success has been limited due to an unclear understanding of the intrinsic properties of Zn2⁺ and proton (H⁺) insertion into MnO2. This study investigates the predominant phases of MnO2—α, β, δ, and γ—and elucidates their reaction mechanisms using first-principles computational methods based on density functional theory (DFT). Our research reveals that H⁺ ions exhibit a higher initial insertion voltage compared to Zn2⁺ ions, but their diffusion in MnO2 is significantly impeded by strong interactions with oxygen. Additionally, H⁺ insertion partially obstructs Zn2⁺ ion migration. Furthermore, the insertion of Zn2⁺/H⁺ and the adsorption of H⁺ on the MnO2 surface are intricately linked to the dissolution process of manganese. This work significantly enhances our fundamental understanding of MnO2 as a cathode material for AZIBs.