Irritable bowel syndrome is a disorder of gut–brain interaction characterized by recurrent abdominal pain and altered bowel habits. Interactions among intestinal microorganisms and their metabolites, the epithelial barrier, mucosal immunity, and gut–brain signaling provide important insights into the heterogeneity of this condition. Engineered micro- and nanoscale carriers may improve the stability of orally administered bioactive agents and facilitate local intestinal delivery while modulating relevant pathological processes through protection of viable microorganisms, delivery of microbial metabolites, or direct regulation of host cells. This review examines major mechanisms underlying microbiota–immune interactions and summarizes advances in colon-targeted delivery, protective carriers for probiotics, plant-derived vesicle-like preparations, and microalgae-based hybrid systems. We further discuss the biological characteristics of different clinical subtypes and key translational challenges, including safety, quality control, and rigorous verification of therapeutic efficacy. In particular, evidence from direct irritable bowel syndrome studies is distinguished from findings in symptom-based models, other disease models, and fundamental mechanistic experiments.