This study focused on the effects of methylation and different anions (Br − and Cl − ) on the physicochemical and thermal properties of [C 16 MIM]X and [C 16 MMIM]X, belonging to the imidazolium-based ionic liquid (IL) family. The effect of methylation on the transmittance in the fingerprint region of the Fourier transform infrared (FT-IR) spectrum was observed as a blue shift, and a new peak associated with the C-N stretching bond was obtained. In contrast, in the functional group region, the frequency shift was related to the change in the vibrational mode from C2-H-X to C2-methyl-X. In general, methylation resulted in an increase in decomposition temperature, an increase in melting temperature, and a decrease in melting enthalpy, leading to a reduction in entropy. The trends observed for the decomposition temperature, melting temperature, and melting enthalpy with different anions depended on the strength of the Brønsted acids and hydrogen bonds of the Br − and Cl − based anions. The thermal conductivity of the methylated ILs increased with an increase in temperature. In contrast, for the non-methylated (protonated) ILs, the thermal conductivity of [C 16 MIM]Br decreased with an increase in temperature, while the opposite trend was observed for [C 16 MIM]Cl. The data were compared with those of the short alkyl chain and weakly coordinating anion of NTf 2 . The analysis was performed considering different phases, the prominent role and different behaviour in the hydrogen bonding at the C2 position of the imidazolium ring upon methylation, and the significant change in viscosity, which can influence the IL structure.