Proton-exchange membrane fuel cells enable the portable utilization of hydrogen (H2) as an energy resource. Current electrolytic materials have limitation, and there is an urgent need to develop new materials showing especially high proton conductivity. Here, we report the ultra-fast proton conduction in a novel metal–organic framework, MFM-808, which adopts an unprecedented topology and a unique structure consisting of two-dimensional layers of {Zr6}-clusters. By replacing the bridging formate with sulfate ligands within {Zr6}-layers, the modified MFM-808-SO4 exhibits an exceptional proton conductivity of 0.21 S·cm–1 at 85 °C and 99% relative humidity. Modeling by molecular dynamics confirms that proton transfer is promoted by an efficient two-dimensional conducting network assembled by sulfate–{Zr6}-layers. MFM-808-SO4 also possesses excellent photocatalytic activity for water splitting to produce H2, paving a new pathway to achieve a renewable hydrogen-energy cycle.