Abstract: Objective To explore the characteristics of intestinal flora in children with late onset breast milk jaundice(LBMJ) so as to provide evidence for developing guidelines of LBMJ.Methods 15 children with LBMJ in Urumqi Maternal and Child Health Care Hospital and 15 healthy newborns(control group) in Urumqi postpartum rehabilitation center were recruited as study subjects from November 2020 to April 2021. Their fecal samples were collected, and the differences of intestinal flora between the two groups were analyzed and compared by 16S ribosome DNA(16S r DNA) high-throughput sequencing technology.Results They were significantly different in terms of sampling day, feeding mode, body length and weight between the two groups(all P< 0. 05). There was no difference in terms of the diversity of intestinal flora between the two groups(P>0. 05). Linear discriminant analysis(LDA) effect size showed that Bifidobacterium was the species with significant differences between the two groups.Conclusion The abundance and species of intestinal flora in children with LBMJ are not different from those in healthy newborns. Bifidobacterium plays important roles in both LBMJ group and control group, but whether bifidobacterium affects the occurrence and development of LBMJ needs to be further studied.