Surface quality of LED sapphire substrate influences epitaxy quality greatly, and further influences the performance of LED devices. After the chemical mechanical polishing (CMP) of slurry including Al2O3 abrasive and SiO2 abrasive of sapphire grinding wafer, finally ultra smooth surface of sub-nanometric roughness was achieved with surface roughness reaching 0.101 nm measured by atomic force microscope (AFM) and atomic step morphology was presented. Using Zygo profiler and AFM to observe the variations of surface of sapphire grinding wafer from being polished by Al2O3 abrasive slurry to SiO2 abrasive slurry, the generation reason of atomic step morphology of sapphire surface was elaborated, and the CMP removal mechanism of the sapphire atomically ultra-smooth surface was proposed. Through controlling the process conditions of sapphire polishing, a-a type and a-b type atomic step periodic morphologies were obtained respectively. The experimental result shows the chemical reaction speed of double-atom layer 6H1, 6H2 of different adsorptive energy between layers is slightly different. When the revolving speed is relatively slower and mechanical effect Rm is slightly weaker than chemical effect, the difference of chemical reaction speed Rc of different double-atom layer is also presented, and mechanical removal only acts on softening double-atom layer with sapphire polishing surface presenting step morphology of different width of a-b type; while when the revolving speed is relatively faster and mechanical effect Rm is slightly stronger than chemical effect, the mechanical removal speed of each double-atom layer is the same with sapphire polishing surface presenting step morphology of the same width of a-a type.