Previously, we have found that full protonation of the two pyridyloxyl groups of 1,7-bispyridyloxyl-N,N′-bis(2-ethylhexyl)perylene diimide (PDI) (molecule 1) leads to formation of highly fluorescent nanospheres, due to formation of 1,7-bis(4-oxylpyridinium chloride) dramatically enhancing the inter-chromophore interactions in the bay-region (J. Am. Chem. Soc., 2011, 133, 11022–11025; Chem.–Eur. J., 2012, 18, 12305–12313). Molecular modeling revealed that the two pyridyloxyl groups in molecule 1 pointed outside the same facet of the PDI plane, forming a rigid PDI-based bolaamphiphile. In order to more fully investigate the effects of the molecular solvophobicity on the bay-region vs. the molecular solvophilicity including that from the imide-direction and from the solvophilic PDI unit, Fsolvophob/solvophil, on fine-tuning nanomorphologies and properties, we reduced the molecular solvophilicity by replacing the two 2-ethylhexyl (EH) tails in molecule 1 with two shorter cyclohexyl (CH) tails, while maintaining the two 1,7-bispyridyloxyl units, forming molecule 2. Furthermore, we replaced one pyridyloxyl group in molecule 2 with another weaker solvophobic 2-methoxyethoxyl unit, forming molecule 3 to tune the molecular solvophobicity in the bay-region. Morphological studies demonstrated that molecule 2 formed 70–400 nm sized hollow nanospheres in a polar solvent mixture of dichloromethane (DCM)–ethanol (EtOH) and ∼100 nm sized hollow nanoparticles in a weak apolar environment of DCM–methylcyclohexane (MCH) mixture with RMCH = 10–40% (v/v). Upon a further increase of the surrounding apolarity by increasing the RMCH, plate morphologies of nanorods and microplates formed, accompanying with the π–π-stacking changing from the co-facial mode to slippage mode. Differently, molecule 3 always formed platelike nanostructures such as nanotapes in DCM–EtOH mixtures and nano-rhombuses in DCM–MCH mixtures with the molecules adopting co-facial π–π-stacking in both nanostructures. Taken together, the self-assembly and the final nanomorphologies of the PDI-based bolaamphiphiles are both significantly controlled by a small change of Fsolvophob/solvophil and such a leverage effect of the control from Fsolvophob/solvophil is amplified by changing the solvent polarity, for example, fine-tuning REtOH and RMCH.