The sapphire surface morphology, atom removal rate, temperature, polishing force, subsurface damage, dislocation, and stress were explored under different ultrasonic directions, frequencies and amplitudes through molecular dynamics (MD). For both vertical and horizontal vibration, the rising ultrasonic frequency and amplitude will reduce the tangential and normal force, and increase the subsurface temperature and the material removal rate (MRR). Higher frequencies promote the basal dislocation, thus reducing the subsurface damage. Higher amplitudes cause thinner subsurface damage layer under horizontal vibration. However, it is opposite at vertical vibration. The horizontal vibration can obtain a flatter polished surface and a thinner subsurface damage layer due to the longer trajectory and less impact on sapphire surface. This study can provide reference for sapphire high-quality polishing.