In-situ engineering multiple-phase transition-metal based electrocatalyst with excellent performances for hydrogen evolution reaction (HER) is still a major challenge in the electrocatalysis field. Herein, the Mo–Ni–Co trimetallic selenide nanorod arrays are synthesized on a plasma-treated Ni–Co foam (MoSe2–NiSe2–CoSe2/PNCF). The synergistic effects of heterostructured crystal interfaces, the formed 1T-2H mixture phases of MoSe2, and the customized morphological design enable high electrocatalytic activity and stability for the hydrogen evolution reaction (HER) in alkaline media. The catalysts require a low overpotential of 38 mV, just above commercial Pt/C electrodes (35 mV), to deliver a benchmark current density of 10 mA cm−2 (j10). The H2 generation amount (2.6 mmol h−1) is much higher than most of the reported transition-metal based electrocatalysts. Numerical simulations attribute the high electrocatalytic activity to the increased Fermi level with multiple heterointerfaces. The catalyst presents a superior long-term electrochemical stability during continuous reactions with a high current density (j100) for over 100 h. The success of enhancing the electrocatalytic performance paves new avenues for in situ engineering transition-metal based electrocatalysts for energy-related applications.