Four synthetic perylene bisimide-based polyaromatic (PA) surfactants with a structural or functional group difference in their attached hydrophilic/hydrophobic substituent side chains were used to probe structure-nanoaggregation relations in organic media by molecular dynamics simulations and dynamic light scattering. The results from the simulated radial distribution functions and light scattering experiments indicate that variation in the structure of side chains and polarity of functional groups leads to significant variations in molecular association, dynamics of molecular nanoaggregation and structure of nanoaggregates. The aggregates of PA surfactant molecules grow to much larger sizes in heptane than in toluene. The aromatic solvent is shown to hinder molecular association by weakening pi-pi stacking, demonstrating the control of molecular aggregation by tuning solvent properties. In aliphatic solvent, the aggregates formed from PA surfactants of aliphatic alkyl groups and phenylalanine derivatives as a side chain usually have a higher solvent accessible surface area to accessible volume ratio (SASA:AV) than that of tryptophan derivatives in their side chains. PA surfactants with an aliphatic functional group in both side chains does not form polyaromatic pi-pi stacking (T-stacking) due to its strong steric hindrance in both solvents. Depending on the nature of the side chains attached, various stacking distributions, aggregation sizes, and SASA:AV ratios were obtained. In PA surfactant nanoaggregates, all of the solvent molecules were found to be excluded from the interstices of the stacked polyaromatic cores, regardless of whether the solvent molecules are aliphatic or aromatic. Although the change in the structure of side chain substituent in polyaromatic surfactants has a negligible impact on their self-diffusivity, it can strongly influence their intermolecular interactions, leading to different aggregate diffusion coefficients.