Compared with Thermus thermophilus HB8 xylose isomerase(TthXI), the increase of the substrate specificity on D-xylose of its N91D mutant (TthXI-N91D) was observed in the previous study. In order to clarify the structural mechanism of TthXI-N91D, the complex model of TthXI with D-xylose was constructed by molecular docking method. The TthXI-N91D homology model was built by WATH IF5.0 based on the above complex. The results indicate that the distance between the conserved residue H53 NE2 and D-xylose O5 has decreased in 0.083 nm in the TthXI-N91D active site. The short distance is propitious to transfer the hydrogen atom during the open ring process of substrate. At the same time, the distance between the conserved residue T89 OG1, involving in combining glucose, and D-xylose C5 has reduced 0.133 nm. The shrunken space has an unfavorable effect on accommodating the larger glucose than xylose, and lead to the enhanced specificity for D-xylose.The above phenomenon maybe the main reason for explaining that TthXI-N91D is easy to combine D-xylose showing enhanced specificity. The results paly an important role in understanding the catalytic mechanism of xylose isomerase and provides the base for its molecular design.