AbstractWheat flour proteins are subject to oxidation reactions during production, processing and storage. The quality of protein and the rheological properties of wheat are crucial for the flour industry. However, the impact and mechanism of protein oxidised on wheat flour quality remain unclear. In this study, ozone was used to oxidise wheat grains, the secondary structure of protein in flour and the rheological properties of dough were analysed by FTIR and Mixolab. The proportion of α‐helix and β‐folding of protein were decreased significantly, as were the development time (DDT), stability time (DST) and protein weakening (C2) value of dough. Meanwhile, starch gelatinisation (C3), amylase activity (C4) and retrogradation (C5) were increased significantly, along with the elastic modulus (G′) and viscous modulus (G″). Microstructure analysis indicated that protein oxidation destroyed the gluten network structure in the dough. In addition, the L* value of dough was decreased and a* and b* values were increased significantly. The results showed that the oxidation of protein reduced the stability of protein secondary structure, weakened the structure and stability of the gluten network in dough, and changed the viscoelasticity and colour of dough. Overall, these findings provide a better understanding of rheological behaviour in wheat flour.