Ionic liquid crystals have received increasing interest due to their positional and/or orientational order as well as the freedom in molecular motions that arise from the formation of mesophases between solid and liquid. While phase changes of non-fluorinated ionic liquids have been widely reported, there have been few reports on the temperature-dependent phase behavior of fluorinated ionic liquids. Here, we present a series of fluorinated ionic liquids with methylimidazolium cations bearing 1H, 1H, 2H, 2H-perfluoroalkyl chains (butyl, hexyl, and octyl) and halide counterions, and demonstrate their thermotropic mesomorphism. These cations were synthesized under solvent-free conditions, and anion exchange was used to vary the halide counterion. The thermal behavior of the compounds was studied using thermogravimetric analysis and differential scanning calorimetry, revealing both liquid crystalline phases and solid-solid phase transitions. We discovered that the mesomorphic properties of the ionic liquids depend strongly on the length of the perfluoroalkyl pendants. Specifically, ionic liquids with a fluorinated butyl chain showed no mesophase behavior while those with hexyl and octyl fluorinated chains displayed liquid crystalline phases at temperatures above 100 °C. The mesophases were further characterized by polarized optical microscopy and powder X-ray diffraction, highlighting the impact of the fluorinated alkyl chain length.