Molybdenum disulfide quantum dots (MoS2 QDs) have drawn increasing attention owing to their distinct optical properties and potential applications in many fields such as biosensing, photocatalysis and cell imaging. Elucidating the relationship between the surface chemistry of MoS2 QDs and their optical properties as well as biological behaviors is critical for their practical applications, which remain largely unclear. Herein, by adopting a sulfur vacancy modification strategy, a toolbox of MoS2 QDs functionalized with different thiolate ligands was prepared. The effect of surface chemistry on the optical properties of MoS2 QDs was systematically explored by various spectroscopic techniques, revealing the important role of surface ligands in defining their absorption band gap and luminescence quantum yield. Furthermore, cellular experiments showed that the cytotoxicity and intracellular fate (i.e., lysosomal accumulation) of MoS2 QDs are closely related to the properties of surface ligands. Our results underscore the important roles of surface ligands in regulating the properties and biological interactions of these QDs, which will facilitate the future development of MoS2-based materials with precisely controlled functions for biomedical applications.