Water, in addition to acting as a solvent, plays a constructional role in aqueous self-assembly. The hydrophobic molecule of POSS-PDI-POSS (POSS = polyhedral oligomeric silsesquioxanes, PDI = perylene diimide) has a shape anisotropy in which POSS is a ball-like bulky group and PDI is a flat aromatic group. The self-assembly of this molecule in water created assemblies with inner spaces due to the steric effect, which suppressed aromatic interactions of PDI and trapped water for the colloidal stability. By replacing POSS with dodecyl (C12), C12-PDI-C12 aggregated with extended aromatic interaction of PDI and less inner water. The resulting aggregates tended to agglomerate and precipitate. This discovery extended the scope of aqueous self-assembly by using the building blocks without amphiphilicity and created knowledge for biophysics.