The invention relates to a surface treatment method of a sapphire substrate and a crucible therefor. The method comprises the following steps: placing a sapphire substrate on a crucible; carrying outannealing treatment, wherein the surface of the sapphire substrate is an atomic-scale step. By means of the method, the contact area of the sapphire substrate and the crucible is controlled to be smaller than or equal to 2% of the single-side surface area of the sapphire substrate; so that the distribution of heat and air flow on the surface of the sapphire substrate in the annealing treatment process is more uniform; therefore, the sapphire substrate with atomic-scale steps on the surface is obtained. The method is high in repeatability, meanwhile, the invention further provides a crucible for surface treatment of the sapphire substrate, the crucible comprises a cylindrical shell with one end being an open end, the open end is used for containing the sapphire substrate, and therefore thetreatment effect and efficiency of the surface treatment process of the sapphire substrate are higher.