The basal plane of molybdenum disulfide (MoS2) was recently activated for hydrogen evolution reaction (HER) by creating sulfur (S) vacancies (MoS2-x). However, the HER activity of those S-vacancies depends on the concentration of S-vacancies, imposing a dilemma for either improving activity per site or increasing overall active site density. Herein, we use density functional theory (DFT) calculations and experiments to show that the HER activities of MoS2-x are greatly enhanced by adding cobalt (Co) clusters on the basal plane. Our DFT results show that the highest HER activity is achieved when the Co clusters are anchored on the S-vacancies with the interface of Co-Mo as the preferred active site. Our experiments confirm that the addition of Co enhances the activity per unit active site and increases the electrochemical active surface area. These results demonstrate the basal plane activity of MoS2-x can be enhanced by decorating S-vacancies with transition-metal clusters.