The purpose of this article was to estimate the effect of Er,Cr∶YSGG laser ablation on the surface crystal structure of human dentin with X-ray diffractometer (XRD). Er,Cr∶YSGG laser with different energy densities were used to ablate human dentin, and XRD was used to analyze the changes of crystal structures, average particle size, and lattice parameters of hydroxyapatite (HA) crystals before and after laser irradiation. The results show that the average size of HA particles in dentin inorganic phase decreased slightly after laser irradiation with different energy densities, but the cell parameters did not change significantly. Based on XRD data, the ellipsoidal HA grain morphology of dentin before and after laser irradiation were obtained by Rietveld full pattern fitting of Popa model. The surface morphology and microstructure of dentin after laser irradiation were observed by scanning electron microscopy. It was found that the surface roughness of dentin increased obviously, there was no stained layer on the surface, no carbonization phenomenon and crack, and no obvious melting phenomenon. This study showed that the inorganic phase did not change after Er,Cr∶YSGG laser ablation of human dentin, HA grains did not recrystallize, and large area melting was not observed on the dentin surface.