Nanoparticle assembly can be controlled by multivalent binding interactions between surface ligands, indicating that more precise control over these interactions is important to design complex nanoscale architectures. It has been well-established in natural materials that the arrangement of different molecular species in three dimensions can affect the ability of individual supramolecular units to coordinate their binding, thereby regulating the strength and specificity of their collective molecular interactions. However, in artificial systems, limited examples exist that quantitatively demonstrate how changes in nanoscale geometry can be used to rationally P. modulate the thermodynamics of individual molecular binding interactions. As a result, the use of nanoscale design features to regulate molecular bonding remains an underutilized design handle to control nanomaterials synthesis. Here we demonstrate a polymer-coated nanoparticle material where supramolecular bonding and nanoscale structure are used in conjunction to dictate the thermodynamics of their multivalent interactions, resulting in emergent bundling of supramolecular binding groups that would not be expected on the basis of the molecular structures alone. Additionally, we show that these emergent phenomena can controllably alter the superlattice symmetry by using the mesoscale particle arrangement to alter the thermodynamics of the supramolecular bonding behavior. The ability to rationally program molecular multivalency via a systems-level approach therefore provides a major step forward in the assembly of complex artificial structures, with implications for future designs of both nanoparticle- and supramolecular-based materials.