Abstract: In order to improve the quality of high-temperature defatted soybean meal, which is the raw material for producing soybean protein powder, and improve the stability and reliability of process control. Under the condition of microwave power of 20 kW, wind speed of 2.5 m/s, and material thickness of 20 mm, the effects of microwave treatment for 4 to 6 min on the moisture content, temperature, total number of colonies, color after water-dissolving and the secondary structure of soybean protein in high-temperature defatted soybean meal were analyzed. It could be used to guide the production and application of high temperature defatted soybean meal for soybean protein powder production. The results showed that: When the microwave treatment time was between 4 and 6 min, the water content decreased at a rate of 1.51%/min; when the microwave treatment time was 5.45 min, the temperature could be controlled at 103 ℃, the killing rate of microorganisms reached 96.8%, and the total number of colonies reached 100 CFU/g; when the microwave treatment time was between 4.62 and 5.45 min, the red value of the aqueous solution were relatively stable, the brightness and yellow value changed slightly, and the color was good; when the microwave time was ≥5 min, the urease activity was negative, which met the requirements of food for infants and children; microwave treatment had a significant effect on the secondary structure of the protein. When the microwave time was between 4.29 and 5.45 min, the α-helix transformed to the β-turn and then disappeared, and the amount of the β-turn increased rapidly; when the microwave time was between 5.45 and 6 min, the β-turn was rapidly transformed to the α-helix; the β-sheet changed only in small amplitudes and was relatively stable during the entire microwave treatment process. Microwave treatment can effectively control the moisture, color, total number of colonies, urease activity of high-temperature defatted soybean meal, and improve the secondary structure of soybean protein, which is of positive significance for improving the quality of high-temperature defatted soybean meal and expanding the application field.