The process of hydrodesulfurization is one of the most important heterogeneous catalytic reactions in industry as it helps with reducing global SOx emissions by selectively removing the sulfur contaminants from commercial fuel. In this work, we successfully combine high-pressure scanning tunneling microscopy and reaction modeling using density functional theory to observe the hydrodesulfurization of methanethiol (CH3SH) on the Co-substituted S edges of a Co-promoted MoS2 model catalyst in situ at near-industrial conditions and investigate the plausible reaction pathways. The active sites on the Co-substituted S edges show a time-varying atomic structure influenced by the hydrodesulfurization reaction rate. The involvement of the edge Co site allows for the C-S bond scission to occur at appreciable rates, and is the critical step in the hydrodesulfurization of CH3SH. The atomic structures of the S-edge active sites from our reaction models match excellently with those observed in situ in the experiments. Operando scanning tunneling microscopy under near-industrial conditions and density functional theory demonstrate that CH3SH hydrodesulfurization occurs via a new methyl transfer pathway on the Co-substituted S edges of a CoMoS model catalyst.