The complex charge storage mechanisms in aqueous MnO2-based supercapacitors have posed significant challenges to a comprehensive understanding of their chemical behavior. In this study, we employed Au-core@MnO2-shell nanoparticle-enhanced Raman spectroscopy, alongside electrochemical analysis and X-ray absorption, to systematically investigate the competitive charge storage chemistry of protons and cations within the inner and outer layers of δ-MnO2 under alkaline conditions. Our findings reveal that δ-MnO2 operates through a dual mechanism: the intercalation and deintercalation of metal cations dominate charge storage in the inner layer, while surface chemisorption of protons governs the outer layer. Notably, cation insertion induces an irreversible phase transition from MnO2 to Mn2O3, whereas the surface redox process involves a reversible transformation among MnO2, MnOOH, and Mn(OH)2. Additionally, spectral evidence, supported by ab initio molecular dynamics simulations, elucidates the structural changes of interfacial water associated with proton-mediated charge storage in the outer layer. Electrochemical analysis further demonstrates that surface charge storage, primarily mediated by a proton-coupled electron transfer mechanism, is the dominant contributor to the overall capacitance. This work not only advances the molecular-level understanding of electrochemical processes in MnO2-based supercapacitors but also highlights the potential for optimizing surface proton-coupled electron transfer mechanisms to enhance capacitive performance.