Molybdenum disulfide (MoS2) is a promising electrocatalyst for the hydrogen evolution reaction (HER) due to excellent stability and low cost. However, the utilization in electrocatalytic hydrogen evolution is constrained by inherent shortcomings, including fewer edge active sites, poor dispersion, and electrical conductivity. In this work, MoS2 was compounded with carbon nanotubes (CNTs), which are known for their high specific surface area and excellent electrical conductivity. These CNTs, laden with oxygen-containing functional groups, provided nucleation sites that facilitated the rapid assembly of MoS2 nanoflowers under hydrothermal conditions within 3 h. Due to their diminutive size (∼300 nm), these nanoflowers possess a large specific surface area and numerous active sites at their edges. Furthermore, MoS2 nanoflowers exhibited a high concentration of intrinsic S-vacancies. This heterojunction material exhibited superior HER properties. In addition, density functional theory simulation further confirmed that the MoS2 with S vacancy and CNT heterojunction electrocatalysts (VS-M/C) provided a fast charge transfer pathway for water electrolysis, and analysis showed that the conduction band minimum and valence band maximum were mainly contributed by the d orbits of Mo and the p orbits of C. This study proffered a novel approach for the engineering of high-performance MoS2-based HER electrocatalysts.