Digestive diseases are multifactorial conditions influenced by genetic predisposition, microbial infections, diet, stress, and drug side effects. Recent advances in research highlight the significant role of the intestinal flora in the development and management of these diseases. This paper provides an in-depth analysis of the interactions between intestinal microecology and digestive disorders such as inflammatory bowel disease and irritable bowel syndrome, emphasizing the importance of intestinal flora balance in maintaining digestive health. It also examines various diagnostic and therapeutic approaches, including the use of probiotics, fecal microbiota transplantation (FMT), and immune-targeted therapies. The complexity of disease prevention and treatment is further explored through discussions of the role of nutrition, stress management, and drug side effects. By evaluating current methodologies and emerging technologies, this work aims to provide a comprehensive understanding of digestive diseases and offer insights into potential future developments in diagnostic precision and personalized medicine.