On January 1, 2020, new International Maritime Organization (IMO) legislation will reduce the maximum sulfur content for marine fuels outside of sulfur emission control areas (SECA) from now 3.50% (m/m) to 0.50% (m/m) to lower the emission of SOx. In order to enable a smooth transition to the new-generation fuels and to cope with a widely diversified spectrum of heavy fuel oils, a comprehensive chemical description of such bunker fuels will become more important to investigate differences which may cause incompatibility with current engines or to avoid a negative impact for the storage stability. Comprehensive two-dimensional gas chromatography with mass-spectrometric detection (GC X GC-MS) has become one of the most potent analytical methods for detailed analysis of hydrocarbon composition in complex petroleum fractions. However, matrices that contain significant amounts of less- or nonvolatile constituents, such as marine fuels, cannot entirely be targeted by gas chromatography alone. In order to extend the application range of a GC X GC high-resolution time-of-flight mass spectrometry platform (GC X GC-HRTOFMS), we applied and compared thermogravimetric analysis (TGA-HRTOFMS) and direct inlet probe (DIP-HRTOFMS) as additional thermal sample introduction techniques. In this study, we investigated five different marine fuels with GC x GC-, DIP-, and TGA-HRTOFMS to analyze volatile as well as residual compounds. Since each of the deployed techniques showed unique advantages and possibilities, the complementarity of the combined approach is demonstrated. The combination of GC x GC-, DIP-, and TGA-HRTOFMS data enabled the generation of comprehensive chemical fingerprints for differentiation and chemical classification.