Abstract: Objective: The risk factors and the role of mother-child gut microbiota in pediatric inflammatory bowel disease (PIBD) remain unclear. We aimed to explore the clinical risk factors associated with PIBD, analyze the gut microbiota characteristics of children and their mothers, and examine the correlation of microbial composition in mother-child pairs. Methods: We conducted a case-control study including children with PIBD and their mothers as the case group, as well as healthy children and their mothers as the control group. Questionnaires were used to collect information such as family illness history, and maternal and early-life events. Fecal samples were collected from the children and mothers for microbiota 16S rRNA sequencing, to analyze the composition and its potential association with PIBD. Results: A total of 54 pairs of cases and 122 pairs of controls were recruited. A family history of autoimmune disease and antibiotic use during pregnancy were associated with an increased risk of PIBD, and a higher education level of the father was associated with a decreased risk of PIBD. Children with IBD and mothers exhibited different gut microbiota compared to healthy children and mothers. Similarity was observed in the gut microbiota of mothers and children in the same groups. Some bacterial biomarkers of mothers discovered in this study had the power to predict PIBD in their offspring. Conclusion: PIBD is influenced by maternal risk factors and has unique gut microbiota characteristics. Mother-child gut microbiota are closely related, suggesting transmission and influence of gut microbiota between mothers and children. This study provides a potential pathogenesis of PIBD and a basis for developing targeted interventions.