<p>Comprehensive characterization of petroleum-derived sulfur compounds is crucial for researching and developing desulfurization catalysts, equipment, and processes. However, the complex composition and low concentration of sulfur compounds in oils make it challenging for molecular-level separation and characterization. In this work, sulfur compounds in the straight-run diesel fraction were selectively separated from the oil by the methylation/demethylation method, effectively yielding high-purity thiophenes and sulfides. Molecular-level compositional and structural characterization of sulfur compounds was accomplished through comprehensive two-dimensional gas chromatography (GC × GC) coupled with time-of-flight mass spectrometry. The separation significantly enhances the detection sensitivity for low-content sulfur compounds, thereby enabling a more comprehensive characterization of their molecular compositions and structures. Sulfur compounds with diverse skeletons and carbon numbers were tentatively characterized, including 1~3 cyclic sulfides, thiophenes, benzothiophenes, dihydrobenzothiophenes, dibenzothiophenes, tetrahydrodibenzothiophenes, phenanthrothiophenes, and benzonaphthothiophenes. Additionally, hundreds of individual sulfur compounds were characterized by mass spectrometry. Quantitative analysis for individual compounds and compound types was conducted using a flame ionization detector.</p> Graphical Abstract <p></p>