Accurate identification of active sites is highly desirable for elucidation of the reaction mechanism and development of efficient catalysts. Despite the promising catalytic performance of thiolated metal nanoclusters (NCs), their actual catalytic sites remain elusive. Traditional first-principles calculations and experimental observations suggested dealkylated S and dethiolated metal, respectively, to be the active centers. However, the real kinetic origin of thiolate etching during the electrocatalysis of NCs is still puzzling. Herein, we conducted advanced first-principles calculations and electrochemical/spectroscopic experiments to unravel the electrochemical etching kinetics of thiolate ligands in prototype Au25(SCH3)18 NC. The electrochemical processes are revealed to be spontaneously facilitated by dethiolation (i.e., desorption of -SCH3), forming the free HSCH3 molecule after explicitly including the solvent effect and electrode potential. Thus, exposed under-coordinated Au atoms, rather than the S atoms, serve as the real catalytic sites. The thermodynamically preferred Au-S bond cleavage arises from the selective attack of H from proton/H2O on the S atom under suitable electrochemical bias due to the spatial accessibility and the presence of S lone pair electrons. Decrease of reduction potential promotes the proton attack on S and significantly accelerates the kinetics of Au-S bond breakage irrespective of the pH of the medium. Our theoretical results are further verified by the experimental electrochemical and spectroscopic data. At more negative electrode potentials, the number of -SR ligands decreased with concomitant increase of the vibrational intensity of S-H bonds. These findings together clarify the atomic-level activation mechanism on the surface of Au25(SR)18 NCs.