Zero-dimensional MoS2 quantum dots (QDs) possess distinct physical and chemical properties, which have garnered them considerable attention and facilitates their use in a broad range of applications. In this study, we prepared monolayer MoS2 QDs using temporally shaped femtosecond laser ablation of bulk MoS2 targets in water. The morphology, crystal structures, chemical, and optical properties of the MoS2 QDs were characterized by transmission electron microscopy, X-ray diffraction, Raman spectroscopy, X-ray photoelectron spectroscopy, UV–vis absorption spectra, and photoluminescence spectra. The analysis results show that highly pure, uniform, and monolayer MoS2 QDs can be successfully prepared. Moreover, by temporally shaping a conventional single pulse into a two-subpulse train, the production rate of MoS2 nanomaterials (including nanosheets, nanoparticles, and QDs) and the ratio of small size MoS2 QDs can be substantially improved. The underlying mechanism is a combination of multilevel photoexfoliation of monolayer MoS2 and water photoionization–enhanced light absorption. The as-prepared MoS2 QDs exhibit excellent electrocatalytic activity for hydrogen evolution reactions because of the abundant active edge sites, high specific surface area, and excellent electrical conductivity. Thus, this study provides a simple and green alternative strategy for the preparation of monolayer QDs of transition metal dichalcogenides or other layered materials.