Gut microbes are closely associated with most human health. When ingested orally, probiotics can effectively regulate the composition and quantity of human intestinal microorganisms, which is beneficial to human health. However, probiotics will be affected by the harsh environment of the digestive tract during the in vivo transportation process, and ensuring the viability of probiotics is a great challenge. Probiotic encapsulating technology provides an effective solution to this problem. The introduction of extreme temperatures, large probiotic microcapsule sizes and the difficulty in controlling probiotic microcapsule particle sizes mean that traditional microcapsule encapsulation methods have some limitations. From traditional microcapsule technology to the bulk encapsulation of probiotics with nanofibers and nanoparticles to the recent ability to wear nano "armor" for a single probiotic through biofilm, biological membrane and nanocoating. Emerging probiotic nanoagents provides a new conceptual and development direction for the field of probiotic encapsulation. In this review, we presented the characteristics of encapsulated probiotic carrier materials and digestive tract transport systems, we focused on the encapsulation systems of probiotic nanoagents, we analyzed the shortcomings and advantages of the current agent encapsulation systems, and we stated the developmental direction and challenges for these agents for the future.