A series of Ru‐based catalysts have been developed for the hydrogen evolution reaction (HER) by the facile impregnation of copious and eco‐friendly bacterial cellulose (BC) with Ru(bpy)3Cl2 (bpy = 2,2′‐bipyridine) followed by pyrolysis. After the oxidation and molecular recomposition processes that occur within the BC precursors during pyrolysis, sub‐2 nm Ru nanoparticles (NPs) and atomic Ru species confined within surface‐oxidized N‐doped carbon nanofibers (CNFs) can be observed in the derived catalysts. The surface oxidation of CNFs leads the derived catalysts with super hydrophilicity and water‐absorbing capacity, and also provides dimensional confinement for the nanoscaled and atomic Ru species. With these added structural advantages and the component synergy, the derived catalysts show superior HER activities, for which the overpotentials are as low as 19.6 mV (1 m KOH) and 55.0 mV (0.5 m H2SO4) for the most active case at the current density of 10 mA cm−2. Moreover, superior HER activity can be also achieved for the catalysts derived with a wide range of Ru loadings. Finally, the influence of Ru NP size on HER activity is investigated by density functional theory simulations. This method provides a reliable protocol for preparing highly active HER catalysts for scale‐up applications.