To address issues such as clumping, spoon adherence, and the formation of powdery packets in puffed corn flour (PCF), this study incorporated three exogenous proteins—egg white powder (EWP), soybean protein isolate (SPI), and whey protein isolate (WPI)—and applied ultrasonication. This treatment improved PCF's physicochemical properties and microstructure. Ultrasonication increased the starch resistance and reduced the short-range ordering of the samples, as evidenced by in vitro digestion results, X-ray diffraction (XRD), and Fourier-transform infrared spectroscopy (FT-IR) data. Unexpectedly, the sonicated samples exhibited an A + V crystal structure with diffraction peaks near 13°,17°, and 19.9°. Furthermore, by using ultrasonication, the addition of EWP, SPI, and WPI raised the samples' water solubility index by 2.97%, 1.05%, and 9.87%, respectively; however, light transmittance decreased by 34.91%, 42.60%, and 25.33%. The agglomerate rate was reduced to zero; ultrasonic treatment also resulted in microparticles that were smaller and exhibited more holes and gaps on their surfaces. Additionally, the samples' breakdown and setback values increased, while their stability and anti-aging qualities decreased. These findings suggest that ultrasound combined with protein treatment significantly enhances the flushing properties of puffed cereal flours and supports their expanded use in the food industry.