Two dimensional layered materials, such MoS2, WS2 and MoSe2, are efficient catalyst electrode material for electrochemical hydrogen evolution reaction (HER). In the present study, Ru and Mn-doped MoSe2 hierarchical 3D nanoflowers were synthesized using colloidal method and the electrochemical activity of the nanoflowers catalyst was investigated. A significant enhancement in the catalytic activity towards the hydrogen evolution reaction (HER) is observed in both Ru (3.4%, 7.2% and 11.4%) and Mn (1.7% and 2.4%) doped MoSe2 nanoflowers. At a current density of 10mA/cm2, the over potential of doped samples has decreased to a remarkable low value of 143 mV for 11.4% Ru and 167 mV for 2.4% Mn from 223mV of un-doped MoSe2. The doped and un-doped samples exhibit Volmer–Heyrovsky mechanism with the Volmer discharge rate-limiting reaction as the calculated Tafel slope lies in the range of 73-91 mV/dec. The charge transfer resistance (Rct) of MoSe2 nanoflower catalyst is decreased with Ru and Mn doping content. The Rct of 210 Ω for un-doped MoSe2 has reach to 66 Ω for 11.4% Ru and to 52 Ω for 2.4% Mn respectively. We demonstrate that the Ru and Mn dopants donate electrons to the conduction band of the host MoSe2 and modify the density of state at Fermi-level. The conductivity of the MoSe2 catalyst is enhanced by Ru and Mn doping and hence the improvement in electro catalytic activity.