The poor activity of molybdenum disulfide (MoS2) basal plane is the key scientific problem to limit efficient hydrogen production. In this paper, MoS2 with single (VS-MoS2) and double sulfur vacancy (VS, S-MoS2) have been constructed and used for water gas shift reaction (WGSR). Results show that the adsorption energy of VS, S-MoS2 for CO molecule is −1.43 eV, which is 28.6 times and 1.1 times than original MoS2 and VS, S-MoS2, respectively. The energy barrier of the rate-determining step in the association mechanism of VS, S-MoS2 is 1.78 eV, which is 21% lower than pristine MoS2. S vacancies are active sites for CO and H2O adsorption. The delocalized electrons enrichment in S vacancies break the electron transfer barrier between the surface and molecules. Sulfur vacancies as medium make electrons continuously transferred to CO and H2O molecules.