In the past few years, ionic liquids (ILs) with cyano-functionalized anions have shown to be improved candidates for electrochemical and separation applications. Nevertheless, only scattered data exist hitherto and a broad analysis of their structure-property relationship has yet to be attempted. Therefore, in this work, a systematic study of the densities, viscosities and refractive indices of imidazolium-based ILs with cyano-functionalized anions was carried out at 0.1 MPa within a broad temperature range (from 278 to 363 K). The ILs under study are based on 1-alkyl-3-methylimidazolium cations (alkyl = ethyl, butyl and hexyl) combined with the [SCN]-, [N(CN)2]-, [C(CN)3]- and [B(CN)4]- anions. The selected matrix of cation/anion combinations allows us to provide a detailed and comprehensive investigation of the influence of the -CN group through an analysis of the thermophysical properties of the related ILs. The results show that, regardless of the cation, the densities decrease with an increase in the number of cyano groups or anion molecular weight. Moreover, for a fixed cation and temperature, the refractive index of the ILs decreases according to the rank: [SCN]- > [N(CN)2]- ≈ [C(CN)3]- > [B(CN)4]-. On the other hand, no clear trend was observed for the viscosity of ILs and the respective number of -CN groups. The viscosity dependence on the cyano-functionalized anions decreases in the order: [SCN]- > [B(CN)4]- > [N(CN)2]- > [C(CN)3]-. The isobaric thermal expansion coefficient, the derived molar refraction, the free volume and the viscosity energy barrier of all compounds were estimated from the experimental data and are presented and discussed. Finally, group contribution models were applied and new group contribution parameters are presented, extending these methods to the prediction of the ILs properties.