Abstract: Probiotic microencapsulation technology is essential for enhancing the gastrointestinal delivery efficiency and the targeted colonization capacity of live bacterial strains, as different materials and fabrication methods enable the construction of microcapsules with distinct characteristics. This review systematically examines the delivery mechanisms, material systems, and advancements in food applications of probiotic microencapsulation. It begins with an elaboration of multiscale encapsulation techniques such as extrusion, internal emulsification, and microfluidic technology, highlighting its advantages and applicable context in delivery mechanisms. Regarding materials, the structural and functional properties, as well as the protective efficacy, of polysaccharides, proteins, and stimuli-responsive smart wall materials are explored. At the application level, it summarizes the key influencing factors and current application status of microcapsules in dairy products, fruit and vegetable beverages, and functional dietary supplements. Finally, the review envisions future research needs, including the development of low-cost, eco-friendly wall materials, personalized strain-material compatibility strategies, and innovations in large-scale continuous manufacturing processes, to facilitate the transition of probiotic microencapsulation from laboratory-scale research to industrial implementation.