A novel triflate (trifluoromethylsulfonate) ionic liquid (IL) thin film (0.08 μm) stationary phase was implemented for use within the second column of a comprehensive GC×GC configuration. The first column in the configuration had a 5% phenyl/95% dimethyl polysiloxane (DMPS) stationary phase with a 0.4 μm film. The DMPS×IL column configuration was used to separate a mixture of 32 compounds of various chemical functional classes. The GC×GC results for the IL column were compared with a commercially available polar column (with a 0.1 μm PEG stationary phase film) used as the second column instead. Additional studies focused on the rapid and selective separation of four phosphorous–oxygen (P–O) containing compounds from the 32-compound matrix: dimethyl methylphosphonate (DMMP), diethyl methylphosphonate (DEMP), diisopropyl methylphosphonate (DIMP), and triethyl phosphate (TEP). van't Hoff plots (plots of ln k vs. 1/T) demonstrated the difference in retention between the P–O containing compounds (with DMMP reported in detail) and other classes of compounds (i. e., 2-pentanol and n-dodecane as representative) using either the IL column or the commercial PEG column. The selectivity (α) of the triflate IL column and the commercially available PEG column were also compared. The IL column provided significantly larger selectivities between DMMP and the other two compounds (2-pentanol and n-dodecane) than the commercial PEG column. The α for DMMP relative to n-dodecane was 3.0-fold greater for the triflate IL column, and the α for DMMP relative to 2-pentanol was 1.7-fold greater for the triflate IL column than for the PEG column.