In order to improve the expression of heat-resistant xylanase XYNB from Aspergillus niger SCTCC 400264, XynB has been cloned into Pichia pastoris secretary vector pPIC9K. The XynB production of recombinant P. pastoris was four times as E. coli, the Vmax and specific activity of XynB reached 2,547.7 μmol/mg and 4,757 U/mg, respectively. And the XynB still had 74% residual enzyme activity after 30 min-heat treatment at 80°C. The van der Waals force analysis in XYNB (ACN89393 and AAS67299), there is one more oxygen radicals in AAS67299 in their catalytic site, indicating that the local cavity is much more free, and it is more optimal for substrate binding, affinity reaction, and proton transfer etc, and eventually increasing enzyme activity. The H-bonds analysis of XYNB indicated that there are two more H-bonds in 33rd Ser of XYNB (AAS67299) than 33rd Ala(ACN89393 ), two H-bonds between Ser70 and Asp67.