Nanoindentation has been widely used for probing the mechanical properties of tooth, especially for characterizing its complex hierarchical structures. Previous studies have confirmed the anisotropic mechanical behaviors caused by the alternated orientations of enamel rods and the alignment of fibril-like hydroxyapatite crystals, but the longitudinal section of enamel, which was composed of parallel-arranged rods, was regarded as a homogeneous continuum as always. In this study, nanoindentation combined with SEM was carried out with the indenter rotating on the longitudinal section of enamel to evaluate the relativity between the nano-mechanical properties and the orientation of indentation impressions. It has been shown that the enamel presented different elastic modulus and hardness with different angles of indenter on its longitudinal section, and its anisotropy was also confirmed by the remarkable asymmetric morphologies of impressions. We observed that the parallel arrangement of crystal fibrils and enamel rods might trigger the expansion of the micro-cracks in preferred orientation, and result in scalene triangle indentation impressions, altering contact areas as well as inconsistent mechanical behaviors. Consequently, it is considered that the longitudinal sections of enamel should be modeled as anisotropic.