Constructing continuous hydrogen bond networks within confined microenvironments is essential yet challenging for developing high-performance crystalline proton conductors. Herein, we demonstrate a ligand isomerism-directed spatial packing strategy for constructing two {P₄Mo₆}-based cobalt frameworks. Employing the linear bridging ligand 4,4'-bipyridine drives the formation of a densely packed three-dimensional (3D) coordination framework (CoPom-3D), severely restricting solvent-accessible free volume. Conversely, the chelating 2,2'-bipyridine ligand blocks multidirectional extension, yielding one-dimensional (1D) coordination chains (CoPom-1D). Crucially, these 1D chains assemble into a 3D supramolecular architecture via strong π–π interactions, creating robust nanoconfined environments. Despite capturing fewer lattice water molecules and possessing lower intrinsic proton concentration than its 3D counterpart, this unique nanoconfinement profoundly alters the local hydrogen bond topology, promoting a more dynamic hydrogen bond environment. Under identical conditions of 50 °C and a relative humidity of 95%, CoPom-1D exhibits a proton conductivity of 1.92 × 10⁻³ S·cm⁻¹, approximately 17 times that of CoPom-3D (1.12 × 10⁻⁴ S·cm⁻¹). Arrhenius analysis yields an apparent activation energy of 0.11 eV for CoPom-1D and 0.49 eV for CoPom-3D. Together with the pronounced humidity dependence and the short water–framework O···O contacts, this low barrier is consistent with a predominantly Grotthuss-type proton transfer mechanism. Although the microscopic water dynamics and solvent reorganization energy were not directly measured, the nanoconfined environment can be proposed to facilitate local hydrogen bond reorganization. These findings demonstrate that regulating supramolecular nanoconfinement and promoting carrier mobility, rather than merely maximizing coordination dimensionality or structural proton density, provide a rational approach for optimizing proton transfer mechanisms in polyoxometalate-based materials.