Control over the self-assembly pathways of small functional molecules is a current trend in supramolecular chemistry, as a variety of metastable self-assemblies with nanostructures distinct from those of thermodynamically stable assemblies can be formed as kinetic products. If such kinetically formed assemblies can be trapped under non-equilibrium conditions, diverse self-organized structures beyond the immediate molecular design may be accessible. The self-assembly of specifically designed amphiphilic π-conjugated molecules in water represents a promising strategy to realize such conditions, wherein strong hydrophobic molecular interactions play an important role. Based on the alkyl-tethered covalent perylene bisimide (PBI) dyad scaffold that can potentially aggregate into one-dimensional supramolecular polymers, herein we demonstrate that an amphiphilic molecular design can open up new self-assembly pathways, which can potentially afford distinct nanostructures in aqueous media. We synthesized amphiphilic PBI dyads that contain one PBI unit functionalized with hydrophobic branched alkyl chains, and one PBI unit functionalized with hydrophilic branched alkyl chains. By changing the composition ratio of the THF/water mixtures, we obtained one-dimensional fibrous and vesicular aggregates as a result of increasing hydrophobic effects. Increasing the temperature of the THF/water mixtures in which fibrous aggregates are preferentially formed subdued the aggregation to entropy control and resulted in the formation of coil- and ring-shaped kinetic nanoaggregates.