Lysinoalanine (LAL) formed during alkaline extraction of rice residue protein (RRPI), which limited its application in the food industry. In this study, the influence of ultrasonication parameters (acoustic power density, ultrasound duration, and ultrasound temperature) on the inhibition of LAL formation and conformational attributes of RRPI during alkaline extraction was elucidated. The results suggested that the acoustic power density substantially modified the chemical interaction forces between RRPI molecules. At a power density of 60W/L, the ionic bonds (14.37%) and hydrophobic interactions (49.28%) reached the maximum, while hydrogen bonds (15.29%) and disulfide bonds (21.06%) reached the minimum. Moreover, acoustic power density at 60W/L caused a decrease of 18.02% and 12.2% in α-helix, and β-turn, respectively, shifting toward β-sheet, random coil, with an increase of 7.31% and 36.16%. Following ultrasonication, the protein particle size distribution curve shifted in the direction of smaller particle size, forming a relatively concentrated and uniform protein distribution. Sonication power, temperature, and time decreased the absolute value of Zeta potential. Furthermore, significant destruction in microstructure was elicited by sonication, which made the structure looser and more microparticles. Pearson correlation analysis suggested that the inhibition in the levels of LAL was most influenced by the increase of sulfhydryl groups and Zeta potential, as well as the reduction of α-helix content, in which the alteration of the total sulfhydryl group content had a great impact on the Zeta potential and the free sulfhydryl group. The principal component analysis demonstrated a notable correlation between the total sulfhydryl group and both the Zeta potential and free sulfhydryl group of RRPI.