In this paper, the influences of hydroxyl groups between interfaces on friction and energy dissipation are investigated by molecular dynamics simulations. The simulation systems include horizontal oriented carbon nanotube and Si substrate. The hydroxyl groups are grafted only on the substrates or between interfaces in different cases. The simulation procedure is as follows. First, the structure of the simulation system is optimized through energy minimization. Then the relaxation is conducted to ensure the the system reaches an equilibrium state. Finally, carbon nanotube moves at a constant speed along the x direction on the Si substrate. The results show that the average friction on carbon nanotube increases significantly due to the formation of hydrogen bonds between interfaces. The number of hydrogen bonds between interfaces increases with hydroxyl group ratio increasing, which is similar to the trend of friction. The chiral angle of carbon nanotube has a certain effect on friction. The friction on the armchair carbon nanotube is larger than on other types of carbon nanotubes. The diameter has an obvious influence on friction. The friction between the interfaces increases with the diameter of carbon nanotube increasing. The reason is that carbon nanotube with a large diameter becomes flattened at the bottom, which leads to the increase of contact area between interfaces. New peaks appear in the phonon state density of simulation system due to the introduction of hydroxyl groups. With the increase of hydroxyl groups ratio, the values of corresponding peaks of hydroxyl groups in the phonon state density become higher, which indicates that the vibration of hydroxyl groups plays a more important role in energy dissipation. When the hydroxyl group ratio on the carbon nanotube and Si substrate reach 10% and 20% respectively, most energy dissipates through the vibration of hydroxyl groups rather than the vibration of the carbon nanotube and Si substrate. The total energy of the system increases with hydroxyl group ratio increasing, and the potential energy of carbon nanotube also increases with the augment of hydroxyl group ratio on the carbon nanotube. However, when the hydroxyl group ratio on the carbon nanotube remains constant, the potential energy of carbon nanotube decreases with the increase of hydroxyl group ratio on Si substrate. This phenomenon becomes obvious when the hydroxyl group ratio is high. The reason can be attributed to the larger interaction between the carbon nanotube and Si substrate. In general, the energy dissipation of the system is related to the total energy, but the energy dissipating through the carbon nanotube may become less with the increase of total energy.