Probiotics have several health benefits to the host. However, low pH in the stomach, various digestive enzymes and bile salts in the intestine threaten their viability and function. Thus, probiotics need to be protected during gastric transit to address challenges associated with low viability and impaired function. At present, probiotic delivery systems with different trigger mechanisms have been constructed to successfully introduce numerous high-viability probiotics to the intestine. On this basis, the application of non-targeted/targeted probiotic delivery systems in different gut microenvironment and the adjuvant therapeutic effect of probiotic delivery systems on other disease were discussed in detail. It is important to also note that most of the current studies in this area focused on non-targeted probiotic delivery systems. Moreover, changes in intestinal microenvironment under disease state and discontinuous distribution of disease site limit their development. Thus, emphasis were made on the optimization of non-targeted probiotic delivery systems and the necessity of designing more precisely targeted ones.