Cation doping into 2D transition metal chalcogenides (TMC) is always interesting and meaningful, due to the possibilities of tuning both the crystal and electronic structures of TMCs. Herein, we used a mixed phase of CoSe/Co9Se8 to facilitate the successful doping of Mo in CoSe crystal lattice. XRD, HRTEM, Raman spectroscopy and EXAFS analyses show a lattice contraction of Mo doped CoSe. Theoretical calculation confirms that Mo doping can lead to the lattice contraction of CoSe, and cause continuity shift of electron density of state toward Fermi level. We also demonstrated in this work, experimentally and theoretically, that the successful tuning of both crystal and electronic structure of CoSe upon on Mo doping leads to enhanced electrocatalytic HER performance in acidic condition. Co0.8Mo0.2Se showed the best HER activity, with only 186.1 mV overpotential needed to achieve 100 mA cm−2 current density and low Tafel slope of 58.7 mV dec-1.