The design of efficient electrocatalysts for hydrogen evolution reaction (HER) suitable for industrial applications remains a challenging task. In this work, Ru clusters were loaded onto WO3 which were grown on carbon nanotubes (WRu/C-JH) using a rapid Joule heating method. The crystal phases of WO3 was transformed, and abundant active sites were exposed during the rapid heating and cooling process. All these modifications contributed to the greatly improved electrocatalytic activity in HER. As tested, in 1 M KOH, it only required an overpotential of 22 mV to reach 10 mA cm−2 and 401 mV to reach a high current density of 1 A cm−2 on WRu/C-JH. Moreover, WRu/C-JH demonstrated excellent stability at 500 mA cm−2 for 100 h. Furthermore, a two-electrode system was constructed to assess overall water splitting performance of WRu/C-JH. This system was capable of reaching 100 mA cm−2 at a low voltage of 1.94 V. The mechanism of the enhancement in HER for as-prepared sample was also deeply discussed.