Semiconducting 2H-phase MoSe2 usually has poor conductivity and does not exhibit satisfactory properties in the hydrogen evolution reaction (HER). The metallic 1T phase can effectively boost the electrocatalytic activity of MoSe2 by adjusting its electronic structure to improve conductivity and intrinsic activity. Here, we report a unique structural 1T/2H MoSe2 with defects, which is successfully prepared by controlling the reaction temperature, achieving synergistic modulation between active sites and conductivity. Defects can afford more electrocatalytic active sites, and the 1T phase can effectively enhance the conductivity and intrinsic activity. Profiting from the coexistence of the 1T phase and defects, 1T/2H mixed-phase MoSe2 shows superior HER electrocatalytic performance, a low Tafel slope (48 mV dec−1) and a small overpotential at 10 mA cm−2 (−192 mV). This work offers additional insight into enhancing the electrochemical activity of MoSe2 and generally layered dichalcogenide-based catalysts by a simple and direct method.