Nanoparticle (NP) assemblies exhibit collective optical, electronic, and magnetic properties that enable applications in sensing, catalysis, energy conversion, and optoelectronics. However, achieving independent control over structural integrity and surface functionality within such assemblies remains a significant challenge in NP self-assembly. Here, we report a modular post-functionalization strategy that decouples structural locking from surface reprogramming in colloidal molecules (CMs). AB_n symmetry CMs assembled from complementary polymer-grafted Au NPs were selected as representative models and reinforced using multivalent N-heterocyclic carbene (NHC)-containing block copolymers. The NHC anchoring segments form robust C–Au bonds, converting initially noncovalent interparticle junctions into covalently bridged connections without perturbing predefined geometries. This multivalent locking reduces interparticle spacing, enhances plasmonic coupling, and significantly improves chemical, ionic, thermal, and mechanical stability, preserving three-dimensional architectures in the dry state. Importantly, separation of anchoring and functional polymer blocks enables independent introduction of amphiphilic and light-responsive surface properties, allowing solvent-dependent plasmonic modulation and reversible light-triggered hierarchical assembly while maintaining discrete CM geometry.