Designing efficient electrocatalysts for hydrogen evolution reaction (HER) is essential to facilitate hydrogen energy applications. Herein, efficient strategies of doping with metal atoms (Ru) and incorporating with conductive carbon-based material (N-doping graphene tubes) have been developed to construct the hybrid electrocatalyst RuW4.6N4@N-GTs, in which, Ru-doped W4.6N4 nanoparticles integrated on the surface of N-doped graphene tubes. RuW4.6N4@N-GTs reveals superior HER activity and good stability, with a low overpotential of 29 mV to deliver the current density of 10 mA cm−2 and a low Tafel slope of 57 mV dec−1. The unique 3D nano-structure morphology of abundant homogeneous RuW4.6N4 nanoparticles supported on conductive N-GTs network carrier contributes to expose more electrochemical active sites, promoting electrolyte transport and gas emission. At the same time, the N-GTs skeleton could prevent the RuW4.6N4 particles from agglomerating and collapsing, thus leading to the superior stability during HER process. The in situ Ru heteroatom doping could cause the directional electron transfer and more nitrogen vacancies, thus modulating the electron structure of catalysts and optimizing the hydrogen adsorption free energy. The synergistic effect of the above merits endows RuW4.6N4@N-GTs with outstanding HER performance for potential applications in the hydrogen production field.