The development of new methodologies for controlling the organization of quantum materials in multiple dimensions is crucial to the advancement of device fabrication. By using a self-assembly route using selected imidazolium ionic liquids bearing long alkyl chains (C(n)Imida, n = 8, 10, 12) as ligands, we have achieved a tunable assembly of quantum-sized gold nanoparticles. The initial stabilizer of the gold nanoparticles was partially or wholly substituted depending on the concentration and alkyl chain length. it it interactions between imidazolium rings also promote the generation of spatially controlled aggregates from the nanometer to micrometer size regimes. In particular, in the case of an imidazolium ionic liquid with decyl chains, gold particles assemble into a core shell spherical superstructure induced by the aggregation of imidazolium ionic liquid molecules during ligand exchange. Conceptually, the assemblies of nanoparticles mimic biological systems and provide strategies for the organization of single-component nanomaterials into functional assemblies for potential applications. Our approach is general and can be applied to other types of nanomaterials for facile manipulation of the assembly processes, permitting an exploration of physicochemical properties as well as technological applications.