The gut microbiota is significant for infants to grow and develop in the early stages of life. The breast milk microbiota directly or indirectly influences colonizing and the development of early infant intestinal microbiota. Therefore, we wanted to study the microbial diversity and correlation between breast milk and the infant gut. By sequencing the 16S rRNA V3–V4 regions of microbiome in infant feces 1, 14, 20, 30, and 90 days after delivery as well as those in breast milk using Illumina NovaSeq, we studied the component of microbiome in both human milk and infant stools, analyzed the diversity of microbiota, and explored the relationship between them. We found that the richest bacteria in breast milk wereAcinetobacter,Stenotrophomonas,Sphingopyxis,Pseudomonas, andStreptococcus, with a small amount ofLactobacillus,Bifidobacterium, andKlebsiella. The infant feces were abundant inBifidobacterium,Escherichia-Shigella,Klebsiella,Streptococcus,Serratia,Bacteroides, andLactobacillus, with a small number ofAcinetobacterandPseudomonas.Acinetobacter,Bifidobacterium,Klebsiella, andLactobacillusappeared in the breast milk and infant feces, suggesting that they were transferred from the breast milk to the infant’s gut.