In this study, a series of ionic liquids (ILs) are evaluated as stationary phases in comprehensive two-dimensional gas chromatography (GC × GC) for the separation of aliphatic hydrocarbons from kerosene. IL-based stationary phases were carefully designed to evaluate the role of cavity formation/dispersive interaction on the chromatographic retention of nonpolar analytes by GC × GC. The maximum allowable operating temperature (MAOT) of the IL-based columns was compared to that of commercial IL-based columns. Evaluation of the solvation characteristics of GC columns guided the selection of the best performing IL-based stationary phases for the resolution of aliphatic hydrocarbons, namely, trihexyl(tetradecyl)phosphonium tetrachloroferrate ([P66614][FeCl4]) and trihexyl(tetradecyl)phosphonium tris(pentafluoroethyl)trifluorophosphate ([P66614][FAP]) ILs. The best performing [P66614][FeCl4] IL-based column exhibited a MAOT of 320 °C, higher than the commercial SUPELCOWAX 10 (MAOT of 280 °C) and commercial IL-based columns (MAOT up to 300 °C). The structurally tuned [P66614][FeCl4] IL stationary phase exhibited improved separation of aliphatic hydrocarbons by GC × GC compared to the commercial columns examined (e.g., OV-1701, SUPELCOWAX 10, SLB-IL60, SLB-IL100, and SLB-IL111).