Organic ligands are necessarily used to stabilize nanoparticles (NPs) in colloid synthesis, and the presence of these ligands in most cases can have adverse effects on heterogeneous nanocatalysis. Therefore, it is crucial to develop efficient methods to remove ligands and study the removal mechanism. In this article, we developed a combined electrochemical method (chronoamperometry (CA) + cyclic voltammetry (CV)), which can completely and efficiently remove thiol ligand from Au NPs to produce cleaned Au/C catalyst. Using the oxygen reduction reaction (ORR) activity as the evaluation criterion for ligand removal, we found that gas atmosphere (O2) plays an important role in the removal process, while the acidity and alkalinity of electrolyte have no effect on the removal efficiency. A proposed thiol ligand removal mechanism along with Au degradation is presented. The results of CA activation at an oxidation constant potential (1.7 V) indicate that oxidation of thiol alone cannot remove thiol ligand. Only if a reduction constant potential of 0.2 V is further applied, the ORR activity of Au/C catalyst will increase, indicating that both the oxidation and reduction processes of Au NPs are crucial for ligand removal. Although the CA method (with an upper potential of 1.7 V and a lower potential of 0.2 V) can efficiently remove the majority of thiol ligand, complete removal of thiol ligand requires further CV activation. Based on the relevant results, a combined electrochemical method (CA + CV) is established. Developing standardized methods for removing ligands on the surface of catalysts is important for obtaining efficient catalysts and is also important for the reproducibility of catalytic results.