Numerous researchers have focused on the relation between kinetic friction and the surface properties of materials, such as their surface roughness and chemical state, because kinetic friction is the loss of kinetic energy at a sliding interface. Contrary to conventional wisdom, recent theory has predicated that, given the fact of phonon energy dissipation, kinetic friction depends on the properties of bulk atoms in a solid, not only on the surface properties. However, this expectation has not been proven. Here we show evidence of this idea via atomic-scale experiments and simulations. We compared the kinetic frictions of isotopically distinct single-crystal diamonds, which differ only in atomic mass, using atomic force microscopy and observed that the friction of 13 C diamond is lower than that of 12 C diamond by approximately 3%. Simulations and theoretical analysis reproduce this result well, suggesting that the lower friction of 13 C diamond originates from the inhibition of the energy-dissipative phonon by a heavier atom mass. This discovery provides a design concept of low-friction materials by tuning the energy-dissipation process with modification of the inner-solid properties; i.e. phonon properties.