Proton conductors are essential for sustainable energy technologies, enabling efficient ion transport in electrochemical devices. Zr-based metal–organic polyhedra (MOPs) offer a distinctive platform as charge-neutral assemblies of cationic cages and Cl− counterions, creating intrinsic ionic microenvironment without acid doping. Here, we establish surface decoration as a powerful strategy to enhance proton transport in structurally distinct Zr-MOP solids, with the magnitude of enhancement dictated by packing structure. Li@UMOP-1 and Li@UMOP-11 exhibit superprotonic conductivities of 2.43 and 4.19 × 10−2 S cm−1, respectively, at 90% relative humidity (RH) and 95 °C, with Li@UMOP-11 representing the highest value reported to date for MOP-based proton conductors. Structural analyses and computations reveal that the topology-dependent positioning of Li+ ions governs water accessibility to the ionic sites. These findings establish packing-guided surface decoration as a design strategy for high-performance proton-conducting MOP solids.