Lysine is the first limiting amino acid in rice nutrition. In order to optimize the determination method of lysine content, this experiment was set up, the acylation time and dye binding reaction time under 300W ultrasonic power were studied by using ultrasonic oscillator instead of common oscillator. The results showed that, when the optimal acylation time was 15 min, and the dye combination time was 90 min has the best effect. Compared with the national standard method, the improved method has a longer acylation time and a shorter dye combination time, and the total determination time is significantly shortened, but the determination results and test accuracy are higher. Using ultrasonic oscillation instead of traditional oscillator oscillation could optimize the determination method of lysine content. In addition, the optimal dynamic clustering method could prevent the uncertainty of artificial classification and optimize the classification scheme.