Sapphire substrates with different crystal orientations are widely used in optoelectronic applications. In this work, focused ion beam (FIB) milling of single-crystal sapphire with A-, C-, and M-orientations was performed. The material removal rate (MRR) and surface roughness (Sa) of sapphire with the three crystal orientations after FIB etching were derived. The experimental results show that: The MRR of A-plane sapphire is slightly higher than that of C-plane and M-plane sapphires; the Sa of A-plane sapphire after FIB treatment is the smallest among the three different crystal orientations. These results imply that A-plane sapphire allows easier material removal during FIB milling compared with C-plane and M-plane sapphires. Moreover, the surface quality of A-plane sapphire after FIB milling is better than that of C-plane and M-plane sapphires. The theoretical calculation results show that the removal energy of aluminum ions and oxygen ions per square nanometer on the outermost surface of A-plane sapphire is the smallest. This also implies that material is more easily removed from the surface of A-plane sapphire than the surface of C-plane and M-plane sapphires by FIB milling. In addition, it is also found that higher MRR leads to lower Sa and better surface quality of sapphire for FIB etching.