Polysaccharide is abundant in nature, but its complex anti-degradation structure limits the process of bioconversion. In recent years, with the rapid analysis of biomass polysaccharide structure and the identification of polysaccharide degrading enzyme, on the basis of different structure of substrate or product requirement, it is possible to imitate the efficient metabolic pathway of microbial polysaccharides, tailor polysaccharides degrading enzyme system, and promote the efficient conversion of biomass. In this paper, the structure composition of neutral polysaccharide (cellulose and xylan), alkaline polysaccharide (chitin and chitosan) and acidic polysaccharide (alginate) were analyzed. Then the structural characteristics and substrate binding patterns of the major degrading enzymes targeted at the three kinds of polysaccharides were summarized. Protein engineering design and customization strategies are also described. The analysis of different functional areas of enzyme molecules can provide targets for further design and modification to obtain high efficiency enzymes in industrial applications. In addition, in terms of the order of microbial extracellular degrading enzymes and their synergistic relationship, complex polysaccharides degrading enzymes can be precisely tailored based on the needs to achieve efficient and high-value degradation transformation of the biomass.