Sulfur compounds in two representative deep crude oils (Ha9, 6598–6710 m; ZS1C, 6861–6944 m) with distinct levels of maturity from Tarim Basin, China, were analyzed by positive-ion electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). The thiophenic and sulfidic compounds were selectively separated from the crude oils with high purity and recovery by the methylation/demethylation approach and further characterized in detail by gas chromatography (GC) coupled with a sulfur chemiluminescence detector (SCD) and GC–mass spectrometry (MS). The two crude oils have a large difference in sulfur compound composition, which are both unique compared to common crude oils. A homologue series of 1,1-dimethylhexahydrodibenzothiophenes, which has been found as highly resistant organic sulfur compounds in diesel hydrodesulfurization, was detected in Ha9 crude oil. This is the first time that these biomarker-like compounds have been identified in crude oil. Thiadiamondoids (1–3 cages) with more structural isomers than reported oils as well as various acyclic sulfides, which probably derived from alkyl sulfides, were identified in the sulfidic fraction of the ZS1C crude oil, which indicates that the crude oil has an unusual geological history. The selective separation technique would offer broad prospects for geochemical research on sulfur compounds in crude oils, including their compound-specific 34S and 13C analyses.