Autoimmune diseases are characterized by systemic or organ-specific damage mediated by autoimmune responses, which occur when the immune system recognizes and attacks self-antigens. Recent studies indicate a rising incidence of autoimmune diseases and a significant correlation between these diseases and intestinal barrier dysfunction. The intestinal mucosal immune system plays an essential role in maintaining intestinal barrier function and immune tolerance. Dysregulation of this system is implicated in the development of autoimmune intestinal diseases, including inflammatory bowel disease (IBD) and celiac disease, as well as extraintestinal autoimmune diseases, such as systemic lupus erythematosus (SLE) and psoriasis. This review summarizes the composition of the intestinal mucosal immune system and its interactions with various organs, including the gut-liver,gut-kidney,and gut-brain axes,along with their mechanistic roles in autoimmune diseases. It elucidates the mechanisms underlying disorders of intestinal mucosal immunity in autoimmune diseases and highlights recent research advances, providing a reference for developing novel treatment strategies targeting intestinal mucosal immunity for autoimmune diseases.