Fluoride is considered a major pollutant of ground water and can cause cytotoxicity in a concentration-dependent manner. This study epigenetically examined the effect of fluoride on early embryos of Kunming mice administered with 0, 20, 60, and 120 mg/L sodium fluoride (NaF) for 30 days. The results showed that NaF repressed oocyte maturation, fertilization and blastocyst formation at low (20 mg/L), medium (60 mg/L) and high (120 mg/L) doses, respectively, compared to the control. Meanwhile, TUNEL assay showed that embryo apoptosis was induced dramatically in blastocyst stage at either low or medium doses, and in 8-cell stage at high dose, compared to the control, suggesting a dose-dependent effect, which was verified by the increasing trancripts of the apoptotic marker gene BAX. Furthermore, the immunostaining displayed global increases of DNA methylation, H3K9me2 and H3K4me2, and no significant changes in H3K9ac with increasing dose, which were consistent with gene expression results, exhibiting general increases of DNMT1, DNMT3a, G9a, LSD1 and MLL1 and a reduction of JHDM2a in transcription and protein levels. More closely, the methylation statuses of two imprinted genes H19 and IGF2 in differential methylation domains were detected by bisulfite sequencing, showing low methylation for H19 and high methylation for IGF2 in NaF-treated groups compared to the control, which corresponded with high expression of H19 and low expression of IGF2 confirmed by qPCR. Collectively, we demonstrated that fluoride epigenetically impaired mouse oocyte maturation and embryonic development, supplying a better knowledge of fluoride in toxicology and a deeper evaluation of its potential influence in physiological and clinical implications.