Ultra-small size metal nanoparticles (u-MNPs) have broad applications in the fields of catalysis, biomedicine and energy conversion. Herein, by means of a ligand-controlled synthesis strategy, series of Ru-based NPs with high dispersity and ultra-small size (marked as u-Ru/C), or sparse and aggregated state (marked as a-Ru/C) anchored on the surface of hollow porous carbon shells are prepared. Systematical in-situ thermogravimetry-mass spectrometry-Fourier transform infrared spectra tests suggest that the different ligands in these Ru-based precursors can regulate the nucleation, growth and fixation of metal sites during the pyrolysis process, thus contributing to Ru NPs with various size and dispersity. As a result, when applied to hydrogen evolution reaction, the u-Ru-1/C catalyst displays a low Tafel slope of 26 mV·dec^-1, overpotential of 31 mV (at 10 mA·cm^-2) and a large exchange current density of 1.7 mA·cm^-2 in 1.0 M KOH, significantly better than that of the a-Ru-2/C, hollow carbon and even commercial 20% Pt/C. This is mainly because that the u-Ru-1/C sample owns both smaller particle size, more electrochemical active sites, higher intrinsic activity and optimized surface H adsorption ability than that of the a-Ru-2/C counterpart. Such ligand-modulated growth strategy is not only applicable to Ru, but also can be extended to other similar metals, offering a step forward in the design and synthesis of highly dispersed u-MNPs.