Abstract: 　Neonatal necrotizing enterocolitis (NEC), childhood inf lammatory bowel disease (IBD), and Hirschsprung-associated enterocolitis (HAEC) are common intestinal inflammatory diseases in pediatrics, which seriously affecting the quality of life of patients and even posing a threat to life. The mechanism is not clear at present. Studies have shown that intestinal inflammatory diseases closely related to the intestinal flora disturbance. However, approximately 85% of the intestine microbiota cannot be cultured. Recently, the high-throughput sequencing technology is developing rapidly, which makes it feasible to explore the intestinal flora comprehensively. This article reviewed the recent advances on the role of intestinal flora in pediatric inflammatory bowel diseases pathogenesis and the application of probiotics.