This article systematically reviews the advances in clinical and basic research on acupuncture and moxibustion for digestive system diseases over the past decade. From the perspective of evidence-based medicine, it synthesizes relevant literatures and research outcomes to clarify the distinctive therapeutic features of acupuncture and moxibustion in irritable bowel syndrome, functional dyspepsia, chronic gastritis, ulcerative colitis and postoperative gastrointestinal dysfunction, and further define its advantageous clinical application scenarios and definitive clinical positioning in the management of these disorders. Furthermore, from multi-disciplinary dimensions including neuroimaging, molecular immunology and microbiomics, this study dissects the key action links and specific molecular targets of acupuncture and moxibustion, and unveils its scientific essence of exerting multi-target integrated regulation via the brain-gut axis and brain-gut-microbiota axis—the core regulatory pathways for the gut-brain interaction. In response to the core bottlenecks in current research, such as high heterogeneity of clinical protocols, poor translational potential of mechanistic research findings and inadequate standardization of clinical evaluation systems, this article puts forward targeted development strategies, including conducting high-quality clinical research on precision acupuncture and moxibustion, constructing a multi-omics integrated mechanistic model based on clinical practice, and innovating a modernized and standardized evaluation system for traditional Chinese medicine. These targeted efforts are intended to advance the innovation of research paradigms and facilitate efficient clinical translation of research achievements in this field.