Two-dimensional gas chromatography with sulfur chemiluminescence detection (GC x GC-SCD) is applied to understand the changes in alkylated thiophenes, benzothiophenes (BTs), and dibenzothiophenes (DBTs) during supercritical water (SCW) upgrading of Arabian Heavy crude oil. It is shown that SCW treatment of heavy crude oil has several important effects: (1) The amount of BTs and DBTs in the distillate range increase, primarily due to cracking of heavier compounds. (2) Most of the long side chains on the thiophenes, BTs, and DBTs crack to form the corresponding thiophenic compounds with shorter side chains. (3) A small amount of the alkylated thiophenes undergo ring closure to form BTs during SCW treatment, and a small amount of the alkylated BTs appear to form DBTs in a similar way. As reported earlier, SCW treatment removes some of the sulfur from the oil phase, presumably as hydrogen sulfide (H2S). Distilling the heavy crude oil into light and heavy fractions and treating these fractions individually with SCW showed these effects more clearly. Model compound studies on hexylthiophenes confirm that SCW cleaves alkyl chains bound to thiophenes.