Ionic and electronic transport in electrodes is crucial for electrochemical energy storage technology. To optimize the transport pathway of ions and electrons, electrode materials are minimized to nanometer-sized dimensions, leading to problems of volumetric performance, stability, cost, and pollution. Here we find that a bulk hexagonal molybdenum oxide with unconventional ion channels can store large amounts of protons at a high rate even if its particle size is tens of micrometers. The diffusion-free proton transport kinetics based on hydrogen bonding topochemistry is demonstrated in hexagonal molybdenum oxide whose proton conductivity is several orders of magnitude higher than traditional orthorhombic molybdenum oxide. In situ X-ray diffraction and theoretical calculation reveal that the structural self-optimization in the first discharge effectively promotes the reversible intercalation/de-intercalation of subsequent protons. The open crystal structure, suitable proton channels, and negligible volume strain enable rapid and stable proton transport and storage, resulting in extremely high volumetric capacitance (~1750 F cm–3), excellent rate performance, and ultralong cycle life (>10,000 cycles). The discovery of unconventional materials and mechanisms that enable proton storage of micrometer-sized particles in seconds boosts the development of fast-charging energy storage systems and high-power practical applications.