The definition of prebiotics has been updated to “a substrate that is selectively utilized by host microorganisms conferring a health benefit”. According to the latest definition, prebiotics have expanded beyond carbohydrates to include substances such as conjugated linoleic acid, plant polyphenols and etc.. The utilization of prebiotics were no longer limited to the gastrointestinal tract, and their applications were not confined to food. This research focused on the various health-promoting effects of prebiotics, including alleviating constipation, promoting bone health, easing obesity, inhibiting pathogenic bacteria, reducing inflammation, and modulating the immune system. The mechanisms by which prebiotics promoted host health were elaborated in depth. These mechanisms were primarily included two aspects. First, prebiotics were directly or indirectly utilized by beneficial microbes of the host, thereby playing a role in modulating the microbial community. Second, the metabolites produced by the microbial metabolism of prebiotics were beneficial to the host's health. In addition, certain oligosaccharides and polysaccharides as prebiotics also had excellent processing characteristics, which positively affected the texture and flavor of food products. Therefore, prebiotics were widely used in food products such as solid beverages, candies, dairy products, and bakery products. However, there were still some issues that urgently needed to be addressed in the efficacy evaluation and application of prebiotics. Among different populations, the intestinal microbiota varied in different physiological states. Thus, differences in gut microbiota inevitably led to differences in the utilization of the same prebiotics. Differences in the structure of prebiotics, such as monosaccharide structure, degree of polymerization, branching, and functional groups, could also affect their utilization by intestinal microorganisms. In summary, targeted application of prebiotics for different population groups based on physiological status and optimization or modification of prebiotics to specific structures would be the key to the precision application of prebiotics.