Exogenous factors influence embryo development. Enniatin B1 (EB1), one emerging mycotoxin of Fusarium fungi, can cause damage to cells and mouse blastocysts. However, the toxicity of EB1 on porcine embryo development and whether melatonin can eliminate the detrimental effects of EB1 on embryos remain unclear. Here, this work demonstrated that EB1 significantly decreased the cleavage and blastocyst rates and blastocyst cell number of embryos in a dose and time dependent manner. Further study displayed that EB1 obviously destroyed nuclear remodeling dynamics. Importantly, EB1 triggered embryo apoptosis through downregulating the expression of Sod1, Gpx4, Cat and Bcl2l1 while upregulating the transcription of Bax and Caspase3. Moreover, EB1 significantly disrupted the transcription of Dnmt1, Dnmt3a, Tet1 and Tet3, further leading to incomplete DNA demethylation of CenRep, Oct4, Nanog and Sox2, thus, the expression of Eif1a, Oct4, Nanog and Sox2 remarkably decreased. Whereas EB1-exposed embryos were treated with melatonin, these disorders were obviously ameliorated, and the development ability of embryos was also rescued. In conclusion, EB1 exerted detrimental effects on porcine early embryos, while melatonin effectively rescued EB1-mediated defects in embryos. This work provides a novel insight into the improvement of embryo quality and the promotion of human and animal reproduction.