Abstract: In order to explore the changing law of the functional characteristics of the gluten-starch composite system after microwave treatment, different microwave powers were used to process the gluten-starch system with different ratios. Afterwards, a texture analyzer was used to determine the gel properties, and a differential method was used to determine water and oil holding capacity. A colorimeter was used to determine the color, and an ultraviolet-visible spectrophotometer was used to determine the extraction rate of gliadin and gliadin. Moreover, the molecular weight distribution of the protein in the composite system was presented by SDS-PAGE electrophoresis, and the secondary structure of the protein was determined by fourier transform infrared spectroscopy. The research results showed that the gluten-starch system with high-gluten flour ratio was strongly affected by the microwave power. With the increase of microwave power, the gel strength and water holding capacity of the high-gluten flour composite system both increased first, when the microwave power was 540 W, its gel strength and water holding capacity began to be weakened, but it was still higher than the non-microwave level, microwave heating reduced the brightness of the high-gluten flour and medium-gluten flour composite systems. At the same ratio, with the increase of microwave power, the brightness of the gluten-starch system decreased significantly, and the redness value and yellowness value first decreased and then increased. The glutenin content first increased and then decreased with the increase of microwave power. Correspondingly, the soluble protein first decreased and then increased. With the increase of microwave power, the content of high molecular weight protein subunits decreased, while, the content of low molecular weight protein subunits increased. Microwave heating of different powers led to changes in the positions of hydrogen bonds at varying degrees, influencing the secondary structure of the gluten-starch system. This study provides a theoretical basis for the application of gluten-starch system in food processing, as well as for the quality improvement of microwave-procession for flour products.