Atmospheric residue from Saudi Arabia (SZAR) was subjected to supercritical fluid extraction fractionation (SFEF) experiments. Four extractable subfractions (SFEF 1−4) and an unextractable end-cut were obtained. SFEF 1−4 were subjected to a hydrotreating (HDT) test in a mini-tubular reactor packed with commercial hydrodemetallization (HDM) and hydrodesulfurization (HDS) catalysts in order to determine the structural composition transformation of sulfur-containing compounds. Experiments were undertaken at a temperature of 360°C, a hydrogen pressure of 14.7 MPa, a liquid hour space velocity (LHSV) of 0.25 h −1 , and a H 2 /feed ratio of 650:1 (m 3 /m 3 ). The SFEF subfractions and their products were subjected to analysis of their sulfur and nitrogen contents, using an ANTEK 7000S analyzer, and their saturates, aromatics, resins, and asphaltenes (SARA) compositions were analyzed using open column liquid chromatography. The detailed molecular composition of sulfur heteroatom species was determined by methylation, followed by positive-ion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI FT-ICR MS). In ESI FT-ICR analysis, the sulfur-containing compounds were characterized in terms of class, type (double bond equivalence, DBE), carbon number distribution, and relative abundance. According to the different number of sulfur atoms, sulfur-containing compounds can be divided into S 1 and S 2 class species. The results show that, depending on different transformation mechanisms, S 1 class species, which have less-aromatic cores, are easy to convert, no matter the side chain length. In addition, S 2 class species with less-aromatic cores and/or less carbon numbers have better hydrogenation reactivities. Meanwhile, S 2 class species with long and/or complex chains would be easy to cleavage into small ones under the reaction conditions. Compare to S 1 class species, S 2 species are more active. The potential transformation of sulfur compounds in HDT of subfractions of atmospheric residua were inferred from the DBE distribution and carbon number data by involving SFEF, methylation followed by FT-ICR MS for sulfur species of SFEF subfractions and their HDT products. The results may help understanding of the heavy oil sulfur removal sequence and catalyst/ process optimization for heavy oil desulfurization and thereby assist the efficient production of clean transporation fuels.