In this study, wheat flour (WF) was modified by annealing (ANN) using plasma-activated water (PAW) for the first time. Compared with WF and DW-WF, the results of scanning electron microscopy (SEM) and particle-size analysis showed that the granule structure of wheat starch in PAW-WF was slightly damaged, and the particle size of PAW-WF was significantly reduced. The results of X-ray diffraction and Fourier transforming infrared spectroscopy indicated that PAW-ANN could reduce the long-range and short-range order degrees of wheat starch and change the secondary structure of the protein in WF, in which the content of random coils and α-helices was significantly increased. In addition, the analysis of solubility, viscosity, and dynamic rheological properties showed that PAW-ANN improved the solubility and gel properties of WF and decreased its viscosity properties and short-term regeneration. PAW-ANN, as a green modification technology, has the potential for further application in WF modification, as well as in the production of flour products.