MoS₂ based materials are considered the most reliable alternative catalysts for the hydrogen evolution reaction (HER), where engineering of active sites has emerged as an acceptable approach to tune their HER activity. In this approach, the dispersion of bulk MoS₂ in the aqueous phase was increased with a surfactant (sodium dodecyl sulfate), which reduced the exfoliation time and enhanced the exfoliation ability to produce layered MoS₂ nanosheets. During the hydrothermal treatment, the nanosheets were further scissored into small nanocrystals. Nanocrystals have attractive properties with stable dispersion and high-water solubility. Our method provides a scalable, eco-friendly, easy, and low-cost strategy for designing other HER catalysts. Such ultra-small MoS₂ nanocrystals with rich Mo vacancies were used as catalysts for HER, which showed excellent electrocatalytic activity with a low overpotential (95 mV) and small Tafel slope (41 mV/dec) in 0.5M H₂SO₄ electrolyte. The design and synthesis of the HER catalyst in this work presents a promising path for preparing active and stable electrocatalysts to replace costly metal-based catalysts for hydrogen production.