A common feature of ionic liquids composed of cations with long aliphatic side chains is structural heterogeneities on the nanometer length scale. This so-called microphase separation arises from the clustering of aliphatic moieties. The temperature dependence of the liquid bulk structure was studied by small-angle X-ray and neutron scattering for a set of methylimidazolium ([C(18)C(1)im](+), [C(22)C(1)im](+)) based ionic liquids with tris (pentafluoroethyl) trifluorophosphate ([FAT)](-)), bis (trifluoromethylsulfonyl)imide ([NTf2](-)), and bis(nonafluorobutylsulfonyl)imide ([NNf(2)](-)) anions. The experimental data is quantitatively analyzed using a generalized Teubner-Strey model. Discussion of the resulting periodicity d and correlation length zeta shows that the structural heterogeneities are governed by the interplay between the alkyl chain length, the geometry of the anion, and entropic effects. Connections between the mesoscopic correlation functions, density, and entropy of fusion are discussed in comparison to alcohols. The observed dependencies allow predictions on the mesoscopic correlation functions based on macroscopic bulk quantities.