The ultrawide band gap of diamond distinguishes it from other semiconductors, in that all known defects have deep energy levels that are less active at room temperature. Here, we present the effect of deep defects on the mechanical energy dissipation of single-crystal diamond experimentally and theoretically up to 973 K. Energy dissipation is found to increase with temperature and exhibits local maxima due to the interaction between phonons and deep defects activated at specific temperatures. A two-level model with deep energies is proposed to explain well the energy dissipation at elevated temperatures. It is evident that the removal of boron impurities can substantially increase the quality factor of room-temperature diamond mechanical resonators. The deep energy nature of the defects bestows single-crystal diamond with outstanding low intrinsic energy dissipation in mechanical resonators at room temperature or above.