Cobalt-promoted molybdenum sulfide (CoMoS) is known as a promising catalyst for H2 evolution reaction and hydrogen desulfurization reaction. This material exhibits superior catalytic activity as compared to its pristine molybdenum sulfide counterpart. However, revealing the actual structure of cobalt-promoted molybdenum sulfide as well as the plausible contribution of a cobalt promoter is still challenging, especially when the material has an amorphous nature. Herein, we report, for the first time, on the use of positron annihilation spectroscopy (PAS), being a nondestructive nuclear radiation-based method, to visualize the position of a Co promoter within the structure of MoS at the atomic scale, which is inaccessible by conventional characterization tools. It is found that at low concentrations, a Co atom occupies preferably the Mo-vacancies, thus generating the ternary phase CoMoS whose structure is composed of a Co-S-Mo building block. Increasing the Co concentration, e.g., a Co/Mo molar ratio of higher than 1.12/1, leads to the occupation of both Mo-vacancies and S-vacancies by Co. In this case, secondary phases such as MoS and CoS are also produced together with the CoMoS one. Combining the PAS and electrochemical analyses, we highlight the important contribution of a Co promoter to enhancing the catalytic H2 evolution activity. Having more Co promoter in the Mo-vacancies promotes the H2 evolution rate, whereas having Co in the S-vacancies causes a drop in H2 evolution ability. Furthermore, the occupation of Co to the S-vacancies leads also to the destabilization of the CoMoS catalyst, resulting in a rapid degradation of catalytic activity.