Xylan and cellulose are the two major constituents in numerous types of lignocellulose. Thus, bifunctional enzyme incorporated xylanase/cellulase activity has attracted considerable attention since it has great cost savings potential. Recently, a novel GH10 family enzyme XynA identified from Bacillus sp. was found to degrade both cellulose and xylan. To understand its molecular catalytic mechanism, here we first solve the crystal structure of XynA at 2.3 Å. XynA is characterized with a classic (α/β)8 TIM-barrel fold (GH10 domain) flanked by the flexible N-terminal domain and C-terminal domain. XynA has a longer N-terminal and C-terminal than most other GH10 family enzymes. The important thing is that the activity of our N-terminal truncated XynA_ΔN37 is significantly improved. And we found that the C-terminus is crucial to protein expression in solution. Protein thermal shift and enzyme activity assays reveal that conserved residues Glu182 and Glu280 are both important for catalytic activities of XynA, which is verified by the crystal structure of XynA with double mutant E182A/E280A. Molecular docking studies of XynA with xylohexaose and cellohexaose, together with site-directed mutagenesis and enzyme activity assay, demonstrate that Gln250 and His252 are indispensable to bifunctional activity. These results elucidate the structural and biochemical features of XynA, providing clues for further modification of XynA for industrial application.