As the human body’s “second genome”, intestinal microecology plays a core role in maintaining host metabolic homeostasis, immune function and intestinal barrier integrity. Gastrointestinal surgery profoundly remodels the composition and function of gut microbiota through multiple approaches, including anatomical reconstruction, changes in digestive physiology and perioperative interventions. In recent years, with the rapid advancement of high-throughput sequencing technology, multi-omics analysis and clinical translational research, the effects of different gastrointestinal surgical procedures on intestinal microecology and their correlations with postoperative complications have been gradually clarified. This article systematically reviews domestic and international research progress on the relationship between major gastrointestinal surgical procedures (such as bariatric and metabolic surgery, radical gastrectomy, colorectal resection and ileostomy) and intestinal microecology. The review is conducted from four aspects: alterations in gut microbial composition, remodeling of metabolic functions, microecological mechanisms of surgical complications, and targeted intervention strategies, aiming to provide microecology-based evidence for clinical practice in gastrointestinal surgery.