Breakage of the C–N bond is a structure sensitive process, and the catalyst size significantly affects its activity. On the active metal nanoparticle scale, the role of catalyst size in C–N bond cleavage has not been clearly elucidated. So, Ru catalysts with variable nanoparticle sizes were obtained by modulating the reduction temperature, and the catalytic activity was evaluated using 1,2,3,4-tetrahydroquinoline and o-propylaniline with different C–N bond hybridization patterns as reactants. Results showed a 13 times higher reaction rate for sp³-hybridized C–N bond cleavage than sp²-hybridized C–N bond cleavage, while the reaction rate tended to increase first and then decrease as the catalyst nanoparticle size increased. Different concentrations of terrace, step, and corner sites were found in different sizes of Ru nanoparticles. The relationship between catalytic site variation and C–N bond cleavage activity was further investigated by calculating the turnover frequency values for each site. This analysis indicates that the variation of different sites on the catalyst is the intrinsic factor of the size dependence of C–N bond cleavage activity, and the step atoms are the active sites for the C–N bond cleavage. When Ru nanoparticles are smaller than 1.9 nm, they have a strong adsorption effect on the reactants, which will affect the catalytic performance of the Ru catalyst. Furthermore, these findings were also confirmed on other metallic Pd/Pt catalysts. The role of step sites in C–N bond cleavage was proposed using the density function theory calculations. The reactants have stronger adsorption energies on the step atoms, and step atoms have d-band center nearer to the Fermi level. In this case, the interaction with the reactant is stronger, which is beneficial for activating the C–N bond of the reactant.