Abstract 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