Alkaline family 11 xylanase has potential economical and environmentally friendly applications in the paper and pulp industry [1, 2]. However, little is known about structural adaptation of family 11 xylanases to alkaline pH, which restricts the improvement of its activity under alkaline condition by directed evolution. In order to understand the molecular basis of pH-dependant activity of family 11 xylanases, we compared the structure of alkaline, neutral and acidic xylanases and analyzed the mutants of alkali-tolerant xylanases Xyn11A-LC from alkalophilic Bacillus sp. SN5. It revealed that alkaline xylanases increased charged residues contents and decreased Ser, Thr and Tyr residues contents to keep active at relatively higher pH. It also indicated that acidophilic xylanases decreased positively charged residues (Lys and Arg) contents and increased negatively and positively charged residues ratio, increased nonpolar residues (Ala, Phe, Trp and Val) and polar amino acids (Cys, Gln and Ser) contents to keep active at lower pH. Between β6 and β7, alkaline xylanases substituted α-helix for coil or turn of non-alkaline enzymes. Compared with non-alkaline counterparts, an inserted stretch of 7 amino acids, rich in charged residues, might be beneficial for enzyme to catalyze under relatively higher pH condition. The positively charged residues were favored on the molecular surface of alkaline family 11 xylanases. The salt bridges were in favor of xylanases adapting to alkaline environment. Mutational analysis of Xyn11A-LC further revealed that six amino acids (E16, W18, N44, L46, R48 and S187) were proposed to render the enzyme active at elevated pH condition. These findings would help to engineer family 11 neutral xylanases with improved activity under alkaline conditions for biotechnological applications.