Naphthalene derived compounds that belong to the polycyclic aromatic hydrocarbons have significant importance in medicinal chemistry owing to their interesting biological activities. The structural knowledge of new naphthalene derived compounds can help in the understanding of their mechanism of action. In this study, we have investigated the molecular and structural landscape of three naphthalene-derived dications, namely, 1,1′-(naphthalene-2,6-diylbis(methylene))bis(3-methyl-1H-imidazolium), 1,1′-(naphthalene-2,7-diylbis(methylene))bis(3-methyl-1H-imidazolium) and 1,1′-(naphthalene-2,6-diylbis(methylene))bis(1-butylpyrrolidinium) as bromide salts. The structural details and non-covalent interactions for these structures were carefully examined using X-ray crystallography. Contributions to crystal packing from various types of intermolecular contacts were investigated and quantified using the Hirshfeld surface analysis. The backgrounds of these differences were analysed in terms of the key factors such as hydrogen bonding, the position of substituents appended on the naphthyl ring, and the presence of aromatic and non-aromatic moieties as substituents. The present work not only demonstrates how the position of the substituent group on the bicyclic ring influences the geometric conformation and overall packing, but also contributes toward a better understanding of how molecules self-assemble with respect to different functional groups (aromatic vs. non-aromatic).