Abnormal brain-gut interaction is considered the core pathological mechanism behind the disorders of gut-brain interaction, in which the intestinal microbiota plays an important role. Microglia are the “sentinels” of the central nervous system, which participate in tissue damage caused by traumatic brain injury, resist central infection and participate in neurogenesis, and are involved in the occurrence of various neurological diseases. With in-depth research on disorders of gut-brain interaction, we could find an interaction between the intestinal microbiota and microglia and that they are jointly involved in the occurrence of disorders of gut-brain interaction, especially in individuals with comorbidities of mental disorders, such as irritable bowel syndrome. This bidirectional regulation of microbiota and microglia provides a new direction for the treatment of disorders of gut-brain interaction. In this review, we focus on the role and underlying mechanism of the interaction between gut microbiota and microglia in disorders of gut-brain interaction, especially irritable bowel syndrome, and the corresponding clinical application prospects and highlight its potential to treat disorders of gut-brain interaction in individuals with psychiatric comorbidities.