Precisely controlling topological distortion in supramolecular architectures while simultaneously integrating functional properties remains a fundamental challenge in coordination-driven self-assembly. Herein, we report a ligand-directed coordination-covalent synergistic assembly strategy for the rational construction of distorted tungsten/copper/sulfur (W/Cu/S) cluster-based supramolecular cubes. The assembly couples pyridyl-Cu(I) coordination with in situ alkyne-sulfur addition in the [Tp∗WS3]- (Tp∗ = tris(3,5-dimethylpyrazolyl)borate) cluster, affording two discrete cubic cages composed of eight {WS3Cu2} cluster vertices. Systematic modulation of linker rigidity and coordination vector length enables programmable topological distortion while preserving the overall cubic framework, establishing ligand geometry as the key determinant of structural deformation. Single-crystal X-ray diffraction and high-resolution electrospray ionization mass spectrometry (ESI-MS) confirm the structural integrity of the assemblies. The third-order nonlinear optical (NLO) properties of the cluster-based cubes were evaluated in solution and in polymethyl methacrylate (PMMA) composite films using the Z-scan technique. While moderate NLO responses were observed in solution, incorporation into polymer matrices leads to a dramatic enhancement of three orders of magnitude, highlighting the functional consequences of ligand-directed structural modulation. This work establishes a geometry-controlled coordination-covalent assembly paradigm for constructing distorted cluster-based supramolecular cages and demonstrates how rational topological design can translate into amplified photonic performance, providing new insights for the development of high-performance cluster-based nonlinear optical materials.