The incidence of intestinal diseases is increasing every year, placing a heavy burden on the world's health and economy. The interaction of immune, microbial, and environmental factors leading to chronic inflammation and immune dysfunction has gradually become a focus of research on the pathogenesis of intestinal diseases. Among them, type 3 innate lymphoid cells (ILC3s) have attracted much attention due to their unique features.This paper has been carefully reviewed to provide a comprehensive overview of the roles of ILC3s in maintaining the homeostasis of intestinal flora. Initially, the effects of various intestinal microbiota, including bacteria, fungi, viruses, and pathogenic bacteria, on the function of ILC3s were introduced in detail. Subsequently, it summarizes how ILC3 imbalance disrupts the intestinal barrier and leads to digestive diseases, including infectious diseases, colorectal cancer, inflammatory bowel disease, and irritable bowel syndrome.By reviewing the role of ILC3s in maintaining the homeostasis of the intestinal flora and the current research status of ILC3s imbalance disrupting the intestinal barrier and leading to digestive tract diseases, this review provides potential immunotherapy targets for the future and offers a basis for the construction of future animal models and the conduct of clinical trials.© 2025 The Author(s). Published by S. Karger AG, Basel.