Methods to investigate the response of hydrocarbons and sulfur compounds to different extents resulting from thermal oxidation of jet fuels refined via the mercaptan oxidation (Merox) process have been developed. Relative comparison of hydrocarbon contents including n-paraffins, isoparaffins, olefins, naphthenes, and aromatics (PIONA) was performed by using comprehensive two-dimensional gas chromatography hyphenated with a quadrupole-accurate mass time-of-flight mass spectrometer (GC × GC−Q-TOFMS). A simple approach for quantification of sulfur compound groups was then developed using both GC × GC and GC hyphenated with flame photometric detection (GC × GC−FPD; GC−FPD). The approach largely separated the sulfur compounds into two distinct regions comprising of lower polarity S1 (thiophenes, thiophenols, thiols, disulfides, sulfides, and alkyl thianaphthenes) and higher polarity S2 (sulfones and phenylsulfides) groups. The reliability of this approach was evaluated using higher resolution GC × GC−FPD, showing less than ±1% error arising from the coelution of minor compounds in GC−FPD analysis. The calibration method was further applied to reduce the error caused by the dependence of analyte contents on the sample dilution effect from ±14% to ±4%. The GC−FPD analysis showed a significant increase in S2 content from 47 to 59% after 113 min oxidation. This approach was then applied for characterization of 15 practical jet fuel samples from airforce bases.