Nanoindentation test method is widely used to measure the material hardness, which is a standard test and the effect of measurement error is limited. However, the measured results of the nano-hardness for the same plane of single crystal materials, such as sapphire, were very different. The possible reason for the difference of nano-hardness is induced by the anisotropy of single crystal materials. In this study, nanoindentation tests were carried out to obtain the nano-hardness of C-plane sapphire. The tests with two different indenter orientations were designed as follow. On C-plane, one edge of the Berkovich indenter was indented parallel to the direction [101‾0], as well as one edge indented perpendicular to the direction [101‾0] for comparison. The average hardness was 25.58 GPa and 29.64 GPa respectively. Molecular dynamics simulation was employed to reveal the generation mechanism of anisotropy in nanoindentation process. The results showed that the distribution of subsurface dislocations and the activation of slip systems were affected by indenter orientations, which resulted in the difference in nano-hardness. When one edge of the Berkovich indenter was indented perpendicular to the direction [101‾0], C-plane sapphire had a stronger ability to resist deformation, showing a higher hardness on the macroscopic level.