Water-extractable arabinoxylan (WEAX) could effectively improve the cereal food quality, while its regulatory effect on wheat starch properties has yet to be well-understood. This study selected the WEAX with different molecular weight (Mw) but same branched degree, and comparatively investigated their effects on the gelatinization and retrogradation behavior of wheat starch. The decreased degree of swelling power, solubility and peak viscosity suggested that low Mw WEAX (L-WEAX) could hinder starch gelatinization more evidently compared with high Mw WEAX (H-WEAX), due to the pronounced inhibition effect on amylose leaching and amylose-lipid complex formation. L-WEAX suppressed the recrystallization of amylose and thus the short-term retrogradation. However, H-WEAX mainly retarded the recrystallization of amylopectin, exerting a more significant inhibition effect on the long-term retrogradation. This study could provide a theoretical basis for enhancing the quality and extending the shelf life of starchy foods by selecting the optimum structure of WEAX.