•The molecular structure of flaxseed mucilage arabinoxylan was deduced.•The relationship of primary structure and conformation was established.•The structures of major flaxseed dietary fibers fractions were compared. The structure of neutral fraction gum from flaxseed mucilage (FM-NFG) was studied for better understanding of the relationship between primary structure and conformation. Based on methylation/GC–MS, nuclear magnetic resonance (NMR) spectroscopy, the structure of FM-NFG was proposed as arabinoxylans. Flaxseed mucilage arabinoxylans contained β-1,4-linked xylose backbones, which were mainly substituted at O-2 and/or O-3 positions by 1–3 sugar residues. The possible branches included → 5)-α-l-Araf-(1 → (17.3 mol%), → 3)-α-l-Araf-(1 → (4.9 mol%), and → 4)-α-d-Glcp-(1 → (3.5 mol%), which were ended with three terminal sugar units: T-β-d-Xylp-(1 → (15.5 mol%), T-α-d-Glap-(1 → (4.5 mol%), and T-α-l-Araf-(1 → (2.6 mol%). The weight average molecular weight (Mw) of flaxseed mucilage arabinoxylans was calculated to be 1747 kDa by static light scattering (SLS), and it exhibited random coil conformation. The proposed structure and conformational models confirmed that different backbone sugar units especially substitution positions directly contributed to the conformational diversity and rigidity of polysaccharide molecules.