Objective: To analyze the effects of feeding methods on dynamic changes of intestinal flora in infants by metagenomics sequencing. Methods: A total of 60 normal full-term neonates delivered in the Obstetrics Department were enrolled. According to different feeding methods, they were divided into a breastfeeding group (n=23) and a formula feeding group (n=37). Total fecal DNA was extracted, sequenced, and analyzed using a high-throughput sequencing platform. The effects of different feeding methods on the establishment and development of intestinal flora in infants were compared. Results: There was no significant difference in Alpha diversity and Beta diversity of intestinal flora between the formula feeding group and the breastfeeding group (P>0.05). At 3 and 12 months of age, the relative abundance of Firmicutes C was higher in the breastfeeding group than in the formula feeding group (P<0.05). At 3 months of age, the relative abundance of Veillonella was higher in the breastfeeding group than in the formula feeding group (P<0.05). At different ages, there was no significant difference in the relative abundance of different dominant bacteria at the species level between the two groups (P>0.05). Conclusion: Feeding methods have certain effects on the evolution and development of intestinal flora in infants. Among them, breastfeeding is more conducive to the establishment of high-abundance intestinal flora and the normal development of intestinal flora.