Human dentin contains millions of tubules, and the distribution and size of tubule is none-homogeneous, which resulting in various mechanical properties. In this study, we utilize a nanoindentor on the human dentin, and a focused ion-beam (FIB) is adopted to prepare the dentin specimen for transmission electron microscopy (TEM) to evaluate the nanostructure of human dentin after the residual impression of the nanoindents. The nanoindentation results show that the loading-unloading curve is continuous and smooth in both the loading and the unloading steps, which suggests that no cracking occurs. As to the TEM specimen, 50 nm thick specimens are prepared by FIB cross-sectioning. The nano-structural observations reveal that nanoindentation induces an atomic re-orientation, and the indent results in the formation of highstress deformation regions beneath the indenter. High resolution images via TEM and diffraction patterns indicate the dentin is poly-crystallized and present anisotropic properties.