The effect of water soluble arabinoxylan (AX) on the dough formation was studied by Farinograph, Extensograph, CLSM, FTIR, DSC and TPA. The dough development time (DDT), stability time (DST) and extensibility were increased due to the addition of AX. CLSM results exhibited a more structured matrix in the dough due to the structuring functionality of AX. Increase of AX from 0 to 3.5% caused higher α-helix from 19.8% to 30.5% while β-sheet and random coil decreased. These changes made the gelatinization temperatures shift to higher value while the pasting viscosities decreased. After baking process, the specific volume of dough with AX was increased by 3.6–8.6% that was manifested by softer crumb firmness during storage period. Higher concentration of AX (5%) formed non-covalent interactions within the gel network, which disrupted the dough structure and interfered with the mechanical properties of dough during baking process.