In summary, we report a coordination-covalent synergistic assembly strategy for the construction of two unprecedented distorted W/Cu/S cluster-based supramolecular cubes (1 and 2) using the precursor A, Cu(I), and angle-defined alkyne-functionalized pyridyl ligands (L₁ and L₂). The approach integrates in-situ alkyne–sulfur covalent bond formation with pyridyl-Cu(I) coordination, generating robust cluster nodes that direct the formation of discrete cubic architectures. Systematic ligand modification enables precise structural control over the resulting assemblies. In particular, replacement of the central benzene unit with a more rigid naphthalene moiety (L₁→L₂) induces a rigidity-dominated distortion mode, establishing a clear structure–geometry correlations in which ligand architecture governs symmetry and distortion behavior without significantly altering overall cage dimensions. Beyond structural regulation, these W/Cu/S supramolecular cubes exhibit intrinsic NLO activity. While moderate nonlinear absorption is observed in solution, incorporation into PMMA matrices results in enhancements approaching three orders of magnitude, underscoring the critical role of solid-state organization in amplifying macroscopic optical responses. This work expands the structural landscape of coordination–covalent supramolecular assembly and provides mechanistic insight into ligand-directed topological control. More broadly, it establishes a direct structure–property relationship linking ligand geometry, supramolecular distortion, and functional optical performance. The combined strategy of rational ligand design and polymer integration offers a viable pathway toward stable, processable, and high-performance cluster-based nonlinear optical materials, advancing design principles for next-generation supramolecular photonic systems.