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In the present work, comprehensive two-dimensional gas chromatography (GC × GC) was combined with chemometrics for qualitative analysis of petroleum. Method development included the evaluation of the main method parameters of flow modulation for the analysis of heavy hydrocarbons. The best performing GC × GC configuration was selected based on the elution pattern of hydrocarbons and the duty cycle of the method. The forward and reverse fill/flush configurations were carefully optimized and compared to ascertain the best conditions for the separation of high-boiling point constituents. It was found that the modulator’s flow path had a significant impact on the elution profile, wherein the flow restrictor geometry played an important role in fine tuning the elution temperatures of the analytes. The reverse fill/flush configuration equipped with a 2 m × 0.10 mm-di restrictor provided the best retention conditions for hydrocarbons in the C20+ range. The modulation parameters, namely 6 s modulation period and 400 ms flush time, ensured a duty cycle above 95%. Additionally, a case study was executed to showcase the potential of using chromatographic red-blue-green (RBG) images for multivariate data processing. The proposed method was based on independent components analysis (ICA), which suggests a gradual transformation of sample composition by evaporation in the simulated weathering experiments.