Background: Daidzein (DAI) is a kind of natural isoflavonic phytoestrogen with estrogenic activity. However, little is known about its influence on early fetal growth in mammalian animals. In this study, we investigated the effects dietary DAI supplementation on early fetal development in sows. To explore the potential mechanisms, the metabolic profiles of amniotic fluid collected at 35 days of gestation (dg) was determined by using metabolomics. Results: Results show that DAI supplementation at a dose of 200 mg/kg significantly enhanced the number of viable embryos at the early gestation stage (P < 0.05). DAI significantly elevated the concentrations of estrogen (E) and insulin-like growth factor-I (IGF-I) in the amniotic fluid (P < 0.05). Moreover, DAI tended to increase the concentration of progesterone, but decrease the concentration of tumor necrosis factor α (TNF-α) in the amniotic fluid (0.05<P<0.10). Interestingly, the activity of glutathione peroxidase (GSH-Px) was higher in the DAI group than in the CON group (P < 0.05). An 1H NMR-based metabolomics analysis identified a number of metabolites in the amniotic fluid, and some critical metabolites such as arginine, creatine, and citrate were found to be significantly elevated upon DAI supplementation (P < 0.05). Importantly, the metabolic pathways involved in arginine and proline metabolisms were found to be significantly affected by DAI. Conclusions: These findings suggested that dietary DAI supplementation may improve embryos survival by improving hormones, antioxidant capacity, and metabolic profiles in the maternal amniotic fluid.