Inflammatory bowel disease (IBD) is a chronic intestinal disorder characterized by an immune response to factors in the intestinal environment. Dysregulation of the intestinal flora may lead to the development of inflammation. Studies suggest that fecal transplants, probiotics, prebiotics, and dietary interventions may play a potential role in reshaping the intestinal flora and treating the disease. MicroRNAs (miRNAs) participate in physiological processes, including cell development, proliferation, and apoptosis. In addition, miRNAs are important in inflammatory processes and play a role in regulating pro- and anti-inflammatory pathways. MiRNA profiles may serve as a diagnostic tool for IBD and prognostic markers for the disease. The relationship between miRNAs and intestinal flora has not been fully elucidated, and recent studies have demonstrated their roles in regulating the intestinal flora and inducing ecological dysbiosis. In turn, the flora can regulate miRNA expression and improve intestinal homeostasis. It is important to continue exploring this relationship. Therefore, the purpose of this review is to analyze the relationship between gut microbiota and miRNAs in IBD and identify possible precision-targeted therapies for IBD.