Inflammatory bowel disease (IBD) influences several million people around the globe, with a high prevalence in North America and Europe. Results from the studies about host-gut microbial interactions demonstrated that gut microbiota plays a critical role in the progression of IBD, and probiotics can significantly improve microflora dysbiosis and inflammatory response caused by intestinal pathogens. However, several limitations existed for the probiotics delivered to the intestine in the free form (non-encapsulated), such as low pH and diverse digestive enzymes in the gastrointestinal tract, etc. To overcome the problems, several probiotic delivery systems were established and verified with effects. Here, the types and applications of probiotics in animal models and clinical studies are firstly reviewed in this paper. Subsequently, various types of probiotic delivery systems are elaborated, containing the well-known microcapsules and hydrogel delivery systems, and the engineered probiotic delivery systems are also introduced. Furthermore, mechanism of action associated with probiotics are illustrated, including maintaining gut microbiota barrier balance, modulating the immune response, and alleviating oxidative stress, etc. Finally, we discussed the relative advantages and disadvantages of different encapsulation methods, as well as future trends for further development of probiotic delivery systems with health benefits.