Abstract: Chitooligosaccharides, which have a variety of biological activities, are the only known basic oligosaccharide widely used in food, agriculture and biomedicine. Chitosanases can cleave the β-1,4 glycosidic bonds in chitosan specifically to form chitooligosaccharides with different degrees of polymerization. Therefore, obtaining chitosanases with good stability is the key for the large-scale enzymatic preparation of chitooligosaccharides. In order to identify the amino acid sites affecting the pH stability of GH46 family chitosanases, the chitosanase from Bacillus sp. DAU101 (optimal pH 7.5) was selected as template and the chitosanase Csn-BAC from Bacillus sp. MD-5 as the research object. By combining homology modeling and sequence alignments, four candidate sites were selected, and the corresponding mutants were obtained (V1: P68A; V2: A137G; V3: A203M; V4: H234E). Compared with Csn-BAC, the thermal stabilities of four mutants showed varying degrees of reduction, while the pH stability was significantly improved. These results indicate that the selected amino acid sites have an obvious effect on pH tolerance, and this strategy is an effective way to modify the stability of chitosanase.