Ruthenium-ion-catalyzed oxidation (RICO) is an approach for investigating the structure of heavy oils by selectively removing aromatic carbon from petroleum fractions, while leaving the structural integrity of aliphatic units intact. Six petroleum vacuum residue (VR) samples originating from various sources were separated into saturate, aromatic, resin, and asphaltene (SARA) fractions. The aromatics, resins, and asphaltenes were subjected to the RICO reaction, and the products were characterized by gas chromatography (GC) and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). The alkyl side chains on aromatic cores of various VRs were significantly different in terms of their contents and carbon number distribution ranges. Normal alkyl side chains were dominant in all VRs; isoparaffin side chains were ubiquitous but in low concentrations, even in severely biodegraded oils. The content of the methyl group was much more than those of other alkyl groups and the content of the side chain decreased with an increased carbon number. For a given VR, the aromatics, resins, and asphaltenes had similar alkyl side chains, especially for aromatics and resins. The archipelago structures were rare, if they existed; nevertheless, asphaltenes appeared to have relatively more archipelago structures than aromatics and resins. FT-ICR MS analysis indicated that many structural moieties, except alkyl side chains, were connected to aromatic cores, which were abundant. The upper limits of the carbon number of alkyl chains determined by FT-ICR MS analysis were much higher than those obtained by GC analysis. For a given VR, the upper limits of the side chain carbon number in aromatics, resins, and asphaltenes were comparable. The relative abundances of short chains and naphthenic structures in asphaltenes were higher than those in resins and aromatics.