Acute pancreatitis (AP) is one of the most common acute abdomen diseases with increasing incidence and substantial healthcare burden. Gut microbiota disturbance, mucosal barrier failure, and bacterial translocation are identified as the dominant cause of infected pancreatic necrosis and high mortality. With the advance of high-throughput sequencing, imbalance between beneficial and facultative pathogenic microorganisms with their metabolic activities in the development of AP has been increasingly recognized, whereas it remains unclear whether dysbacteriosis is the dominant cause of aggravating AP, or merely reflecting different epidemiological or environmental factors at the individual level. This review discussed the alterations of the gut microbiota and their metabolites during AP with detailed molecular mechanisms. Importantly, it highlights microbiome-based medical therapies which influence gut barrier function and immune homeostasis to mitigate inflammatory responses in AP. Our review will provide a novel roadmap of gastrointestinal microecology in AP progression, and contribute to the future development of microbiome-based diagnostic and therapeutic strategies in clinical practice.