<p>Prophylactic ileostomy is a critical measure for preventing anastomotic leakage after low rectal cancer surgery; however, the incidence of diarrhea following stoma reversal remains high, posing a major clinical challenge. Recent studies have revealed that the underlying pathophysiology involves not only anal sphincter dysfunction but also a comprehensive imbalance in the gut microbiota–metabolite–immune axis. This review systematically elucidates the dynamic evolution of the gut microbiome after stoma reversal and its interplay with host metabolism. It further delves into multidimensional pathophysiological mechanisms, including gut dysbiosis, reduced production of short-chain fatty acids, dysregulated bile acid metabolism, and impaired intestinal barrier integrity. In light of recent advances, this article analyzes the clinical characteristics and subtypes of postoperative diarrhea, summarizes precision diagnostic strategies based on multi-omics technologies, and provides an objective assessment of emerging therapies such as probiotics, fecal microbiota transplantation, metabolic interventions, and nutritional support. Finally, the necessity of establishing an integrated multidisciplinary management model is discussed, with the aim of offering new perspectives and a theoretical foundation for improving the quality of life in rectal cancer patients after surgery.</p>