Zwitterionic microcapsules (ZMCs) based on sulfobetaine with tunable hierarchical structures, superior water retention properties, and high proton conduction capacities are synthesized via precipitation polymerization. The incorporation of ZMCs into a Nafion matrix renders the composite membranes with significantly enhanced proton conductivity especially under low humidity. The composite membrane with 15 wt % ZMC-I displayed the highest proton conductivity of 5.8 × 10(-2) S cm(-1) at 40 °C and 20% relative humidity after 90 min of testing, about 21 times higher than that of the Nafion control membrane. The increased proton conductivity is primarily attributed to the versatile roles of ZMCs as water reservoirs and proton conductors for rendering a stable water environment and an additional proton conduction pathway within the membranes. This study may contribute to the rational design of water-retaining and proton-conducting materials.