Colloidal semiconductor nanocrystals, so‐called quantum dots (QDs), are attractive as molecular‐like smart nanomaterials, and their emission and optoelectronic properties in the dispersed state have been actively studied. The construction of supramolecular structures composed of multiple QDs, however, is still challenging. Here, a new strategy to form supramolecular QD structures via self‐assembly of perylene bisimide (PBI) dyes is demonstrated. In a mixed solution, QDs and PBI undergo time‐dependent fusion to form an isolated colloidal QD‐PBI complex or a unique QD‐PBI co‐aggregate composed of QDs arranged along a sheet‐like PBI nanostructure, and these dramatically different supramolecular structures can be controlled by the solvent polarity.