In this study, silver ion (Ag+)-aided laser-desorption ionization coupled to Fourier transform ion cyclotron resonance mass spectrometry was applied to investigate the effects on sulfur-containing compounds after the hydrodesulphurization (HDS) process. For this purpose, three sets of atmospheric residue (AR) and treated atmospheric residue (tAR) samples were analyzed by adding silver nitrate (AgNO3) solution at an optimized concentration ratio of 1:1. Two high-sulfur samples (5.51 and 4.68% each) and one low-sulfur (0.47%) AR sample were studied. The results presented in this study showed that significant changes in the sulfur (S1 and S2) and hydrocarbon (HC) class were observed after treatment of the high-sulfur AR samples. The removal of S1 species with lower double-bond equivalent values (DBE) (DBE < 9), presumably thiophenes and benzothiophenes, was more effective than the removal of S1 species with higher DBE (DBE > 9) values. In addition, the abundance of the aromatic HC class was significantly increased, but the abundance of the nonaromatic HC class was not. In the case of a low-sulfur AR sample, no significant change in HC class was observed after treatment. Therefore, it was concluded that the transformation of benzo- and dibenzothiophene-type compounds to aromatic HCs is the major reaction occurring in the HDS process. The reaction pathways for the transformation were suggested based on the results obtained in this study and previous literature. This study confirms that laser-desorption silver ionization can efficiently ionize the hydrocarbons and nonpolar sulfur-containing compounds present in crude oil.