Endogenous estrogen deficiency usually causes the systemic osteoporosis including the jaw bones. However, it remains unclear whether estrogen deficiency can affect the tooth mineralization. In this study, the classical osteoporotic rat model was established via the ovariectomy, which was subsequently confirmed by the detection of serum estradiol levels and body weights. The mineralization-related assays were performed to observe the potential changes in mineralized tissues of rat lower incisors. The clinical crown length, compressive strength, radiodensity, and calcium content in the ovariectomy group (OVX) were significantly downregulated (P < 0.01), as compared with the sham operation group (Sham). Histological results revealed that OVX incisors presented the thinner predentin structures than Sham incisors. Immunohistochemical staining and western blot assay further demonstrated that the odonto/osteoblast specific proteins (e.g., dentin sialoprotein, runt-related transcription factor 2, osterix, and osteocalcin) in the dentin-pulp complex of OVX incisors were significantly decreased in comparison with Sham counterparts. Together, estrogen deficiency reduces the dentinogenic capacity and calcium deposition in rat incisors, indicating that estrogen plays an important role in the dentinogenesis.