The Ni-Co-Se structures have been widely examined as an electrocatalyst for the hydrogen evolution reaction (HER). Despite the excellent electrical transportability, they suffer from low profusion of active electrocatalytic sites as well as poor long-term durability. Herein, we demonstrated Nickel-Disulfur doping in Ni-Co-Se as an effective method to simultaneously elevate electrocatalytic activity and stability. In this study, the preparation and optimization of the Ni-Co-Se@NiS2 core–shell structure were discussed using hydrothermal and electrodeposition processes. The electrocatalytic activity of the synthesized samples was investigated in both 1 M KOH solution and Seawater. The results of the electrochemical and microstructural investigations showed that the electrodeposition of NiS2 on Ni-Co-Se under the condition of pulsed potential with a frequency of 0.01 Hz by creating a dual micro-nanometric structure with a high edge area, needed only 73 and 81 mV of overpotentials to achieve a current density of 10 mA.cm2 in KOH and Seawater, respectively, as well as continuous stable operation over 30 h. The excellent kinetics with only 1.7 Ω.cm2 charge transfer resistance reached 300 mV overpotential, the high electrochemically active surface area (ECSA) equal to 1900 cm2, and a turnover frequency (TOF) value of 0.160 s−1 at 140 mV indicate the promising electrocatalytic HER performance of the Ni-Co-Se@NiS2 catalyst. This work introduced a novel strategy for the design and synthesis of high-level selenide-based HER catalysts.