Qingke protein rich in restricted amino acids such as lysine, while the uncoordination of ratio of glutenin and gliadin in Qingke protein has a negative impact on its processing properties. In this study, the effect of multiple-frequency ultrasound combined with transglutaminase treatment on the functional and structural properties of Qingke protein and its application in noodle manufacture were investigated. The results showed that compared with the control, ultrasound-assisted transglutaminase dual modification significantly increased the water and oil holding capacity, apparent viscosity, foaming ability, and emulsifying activity index of Qingke protein, which exhibited a higher storage modulus G' (P