Ruthenium (Ru) as a cheaper alternative to Pt has been studied as a viable alternative for the hydrogen evolution reaction (HER) catalyst, however, no single-atom Ru catalyst has been reported for the HER electrocatalysis. Herein, we design and develop the first type of single-atom Ru based catalyst applied for the HER under pH-universal conditions. This binder-free catalyst consists of single Ru atoms anchored to the surface of MoS2 nanosheets array supported by a carbon cloth (Ru-MoS2/CC, Ru in Ru-MoS2: 0.37 wt%). The abundant dispersed single Ru atoms are highly catalytically active, and the MoS2 array supported 3D porous structure offers more opportunities for active sites and serves as co-catalysts for synergetic catalysis, with accompanying enhanced the electrical conductivity of this array-catalyst. Remarkably, the Ru-MoS2/CC exhibits extremely enhanced catalytic activity compared to that of MoS2/CC and possesses good long-term stability. Density functional theory calculations revealed that the improved catalytic activities stem from the synergistic effect between MoS2 and single-atom Ru. This discovery holds a great potential to accelerate the large-scale binder-free application of single Ru atoms in industry.