This work presents an extended study of the thermal behavior of the alkyl and dialkylpyridinium derivatives of the bis­(trifluoromethylsulfonyl)­imide ionic liquid series, using high resolution power compensation differential scanning calorimetry (DSC) equipment. Temperatures, enthalpies, entropies, and the heat capacity change associated with the glass transition, as well as cold crystallization, solid–solid transitions, and melting, are used to evaluate their ability to form a glass and crystallize. The effects of the cation isomerization and the alkyl chain length increase were used to investigate the nature of the irregular thermal behavior of ionic liquids in general and to establish the link between their thermal properties and nanostructuration. The observed V-shape profile of the melting temperatures versus the alkyl side-chain length is interpreted as a consequence of the balance between the initial decrease of the magnitude of the electrostatic interaction and the regular increase of the dispersive van der Waals forces. The observed differentiation between the thermal behavior below and above the critical alkyl size, CAS, is analyzed and compared with the regular behavior of both the n-alkanes and the n-alkanols. Above the CAS, the entropy and enthalpy profiles present trends similar to those observed in the alkane and alcohol series, contrasting with those observed in the molten salts-like region. These results and evidence are a strong support to the interpretation of the effect of the ILs nanostructuration in the physical-chemical properties. We found a great similarity between the thermal behavior of the imidazolium and pyridinium cation core, highlighting the strong ability of ILs to form a nanostructured network with distinguishable polar and nonpolar domains in the liquid phase.