The introduction of impure atoms or crystal defects is a promising strategy for enhancing the photocatalytic activity of semiconductors. However, the synergy of these two effects in 2D atomic layers remains unexplored. In this case, the preparation of molybdenum-doped thin ZnIn2S4-containing S vacancies (Mo-doped Sv-ZnIn2S4) is conducted using a one-pot solvothermal method. The coordination of Mo doping and S vacancies not only enhances visible light absorption and facilitates the separation of photogenerated carriers but also provides many active sites for photocatalytic reactions. Meanwhile, the Mo-S bonds play function as high-speed channels to rapidly transfer carriers to the active sites, which can directly promote hydrogen evolution. Consequently, Sv-ZnIn2S4 with an optimized amount of Mo doping exhibits a high hydrogen evolution rate of 5739 μmol g−1 h−1 with a corresponding apparent quantum yield (AQY) of 21.24% at 420 nm, which is approximately 5.4 times higher than the original ZnIn2S4. This work provides a new strategy for the development of highly efficient and sustainable 2D atomic photocatalysts for hydrogen evolution.