On-surface synthesis is a powerful methodology for the fabrication of low-dimensional functional materials. The precursor molecules usually anchor on different metal surfaces via similar configurations. The activation energies are therefore solely determined by the chemical activity of the respective metal surfaces. Here, we studied the influence of the detailed adsorption configuration on the activation energy on different metal surfaces. We systematically studied the desulfonylation homocoupling for a molecular precursor on Au(111) and Ag(111) and found that the activation energy is lower on inert Au(111) than on Ag(111). Combining scanning tunneling microscopy observations, synchrotron radiation photoemission spectroscopy measurements, and density functional theory calculations, we elucidate that the phenomenon arises from different molecule–substrate interactions. The molecular precursors anchor on Au(111) via Au–S interactions, which lead to weakening of the phenyl–S bonds. On the other hand, the molecular precursors anchor on Ag(111) via Ag–O interactions, resulting in the lifting of the S atoms. As a consequence, the activation barrier of the desulfonylation reactions is higher on Ag(111), although silver is generally more chemically active than gold. Our study not only reports a new type of on-surface chemical reaction but also clarifies the influence of detailed adsorption configurations on specific on-surface chemical reactions.