Abstract: With the in-depth study on the gut microflora, the impact of intestinal bacteria on human health has attracted more and more attention. It has become a research hotspot in life science and medicine, and is considered as an important target of disease control. Prebiotics can regulate the composition and function of intestinal flora and then improve host health. Carbohydrate is the most basic prebiotic. Its unique physiochemical characteristics and gut microbiota-regulating ability make it a promising ingredient for achieving drug target delivery and intestinal health promotion. In this paper, different kinds of prebiotics and their regulation mechanism of intestinal bacteria were illuminated. Moreover, the research progress of carbohydrate prebiotics in drug delivery system was elucidated, and its application prospect is prospected, so as to provide reference for related research.