The layer-dependent properties are still unclarified in two-dimensional (2D) vertical heterostructures. In this study, we layer-by-layer deposited semimetal β-In₂Se₃ on monolayer MoS₂ to form vertical β-In₂Se₃/MoS₂ heterostructures by chemical vapor deposition. The defect-mediated nucleation mechanism induces β-In₂Se₃ nanosheets to grow on monolayer MoS₂, and the layer number of stacked β-In₂Se₃ can be precisely regulated from 1 layer (L) to 13 L by prolonging the growth time. The β-In₂Se₃/MoS₂ heterostructures reveal tunable type-Ⅱ band alignment arrangement by altering the layer number of β-In₂Se₃, which optimizes the internal electron transfer. Meanwhile, the edge atomic structure of β-In₂Se₃ stacking on monolayer MoS₂ shows the reconstruction derived from large lattice mismatch (~ 29%), and the presence of β-In₂Se₃ also further increases the electrical conductivity of β-In₂Se₃/MoS₂ heterostructures. Attributed to abundant layer-dependent edge active sites, edge reconstruction, improved hydrophilicity, and high electrical conductivity of β-In₂Se₃/MoS₂ heterostructures, the edge of β-In₂Se₃/MoS₂ heterostructures exhibits excellent electrocatalytic hydrogen evolution performance. Lower onset potential and smaller Tafel slope can be observed at the edge of monolayer MoS₂ coupled with 13-L β-In₂Se₃. Hence, the outstanding conductive layers coupled with edge reconstruction in 2D vertical heterostructures play decisive roles in the optimization of electron energy levels and improvement of layer-dependent catalytic performance.