Abstract: Probiotics, beneficial active microorganisms for host health, exhibit multiple advantages, such as regulating intestinal microbiota, boosting immunity, and improving metabolism. However, their practical application is hampered by poor stability and low survival rates in harsh environments. Thus, developing a stable delivery system for probiotics is crucial to address these issues. Hydrogels, characterized by their unique 3D network structure and high water content, can effectively protect probiotics against harsh conditions (e.g., gastric acid and bile salts), thereby enhancing their survival rate and bioavailability in the gastrointestinal tract. This review first summarizes the challenges in probiotic application, then elaborates on the encapsulation and protection mechanisms of hydrogels for stable probiotic delivery, and further explores the applications of hydrogel-based probiotics in food and medicine. Furthermore, it highlights the development trend of incorporating artificial intelligence (AI) and machine learning (ML) technologies into probiotic hydrogel delivery systems. The review emphasizes that AI holds significant potential in expanding the application fields, improving stability, and enhancing the functionality of hydrogel-based probiotics. This provides new insights and technical approaches for the in-depth integration and sustainable development of hydrogel-based probiotic delivery systems.