Abstract: Probiotics can easily and largely lose the viability under the undesirable environment, such as food processing, storage, gastrointestinal digestion and so on, which lead to the deficiency of enough amount of viable cells reaching the human colon and exerting its beneficial effect. As the commonly used natural biopolymers in food, proteins and polysaccharides can form macro-, micro- and nano-scale triple-structured probiotics delivery systems through non-covalent or covalent interaction. Hydrogel, microparticles, nanoparticles and other systems have shown the outstanding colon-targeted delivery performance, but more about the approaches and materials of probiotics viability retention need to be further explored. Protein-polysaccharide based delivery systems have been successfully applied in food including yogurt, cheese, beverages and so on, of which scale and structure determine the colon-targeted delivery performance and the improvement level of product quality influenced by the fermentation degree of probiotics. In the future, protein-polysaccharide based delivery system can be further investigated in the aspects of designing highly-efficient-delivery nano structure, multi-functional food with co-encapsulation of other bioactives, packaging materials and novel health food within viable probiotics. With the formation mechanisms of protein-polysaccharide based system as a starting point, this article comprehensively introduces the multiscale structure of the protein-polysaccharide based system for probiotics delivery and its application in food. It can provide references for the development of the protein-polysaccharide based food system within encapsulated viable probiotics.