At present, the frequency and mode of ultrasonic equipment used in most of the studies of ultrasound-assisted enzymatic hydrolysis are single, and the chemical parameters in the process cannot be measured in real time. In this paper, a programmable logic controller (PLC) based control system of S-type ultrasonic-array-assisted enzymatic hydrolysis was designed. The single-, dual-and triple-frequency mode switching of five frequencies was realized, and a mathematical model with ACE (Angiotensin I-converting enzyme) inhibition rate as an index was established by using near-infrared spectroscopy and PLC control. Therefore, the end-point of enzymatic hydrolysis could be determined by real-time on-line in situ monitoring of ACE inhibitory rate. It was found that the predicted value of ACE inhibitory rate was highly correlated with the measured value (R2＞0.84), and the end-point of enzymatic hydrolysis could be controlled automatically.