Comprehensive two-dimensional gas chromatography (GC × GC) is a powerful technique for analyzing mixtures of hundreds of hydrocarbons. In the context of fuel upgrading through selective ring opening, we propose a methodology for GC × GC analysis of complex mixtures resulting from the hydroprocessing of a single model gas oil compound, decalin, over two different types of bifunctional catalysts based on a transition-metal sulfide (NiWS on amorphous silica–alumina) or a noble metal (Ir on La,Na–Y zeolite). The reactions lead to several products families, the dominant ones being ring-opening products (ROPs) and skeletal-isomerization products (SkIPs). First, it is shown that the ROP distribution can be characterized in terms of isomerization degree by using the cumulative distribution function of the GC × GC (GC Image) software. Second, in a more quantitative approach, the products families have been subdivided into chemical groups, according to the isomerization degrees of the individual compounds, which were almost all tentatively identified by two-dimensional gas chromatography coupled with mass spectrometry (GC × GC-MS) through the use of literature data. This allows us to thoroughly analyze the influence of the catalyst nature and the presence of H2S in the reactant feed on the products distribution, and thereby gain insight into the mechanism of decalin hydroconversion over bifunctional catalysts. In particular, it is shown that metal sulfidation suppresses the metal-catalyzed C–C hydrogenolysis pathway at the benefit of undesirable acid-catalyzed isomerization steps. The methodologic work presented here for decalin is believed to be applicable to other bicyclic (naphthenic or aromatic) compounds.