The thermostability of xylanase XynR8 from uncultured Neocallimastigales rumen fungal was improved by combining random point mutagenesis with site-directed mutagenesis guided by rational design, and a thermostable variant, XynR8_VNE, was identified. This variant contained three amino acid substitutions, I38V, D137N and G151E, and showed an increased melting temperature of 8.8 °C in comparison with the wild type. At 65 °C the wild-type enzyme lost all of its activity after treatment for 30 min, but XynR8_VNE retained about 65 % activity. To elucidate the mechanism of thermal stabilization, three-dimensional structures were predicted for XynR8 and its variant. We found that the tight packing density and new salt bridge caused by the substitutions may be responsible for the improved thermostability. These three substitutions are located in the N-terminus, cord and α-helix domains, respectively. Hence, the stability of these three domains may be crucial for the thermostability of family 11 xylanases.