In this work, a temperature-controllable infrared (IR) radiation system with a mechanic stirrer was developed for IR-accelerated enzyme pretreatment of traditional Chinese medicines prior to the extraction of bioactives. The feasibility and performance of this unique system were demonstrated by enzyme pretreatment of Cnidium monnieri, used as the model sample. To investigate enzymatic pretreatment assisted by infrared energy, experiments were carried out to evaluate the effects that enzyme type, pH and the concentration of the enzyme solution, incubation time and temperature have upon the enzymatic activity. Statistical treatment of the results revealed that the selected parameters were all significant. The optimum parameters were obtained as follows: 0.2 mg ml−1pectinase solution, and incubated at pH 6.0 for 2 min at 35 °C. At optimized conditions, the extraction yields of osthole and imperatorin were 18.11 mg g−1and 7.27 mg g−1in pectinase treated sample, increased by 10.2% and 7.9%, respectively, compared with those in the control group. The results also showed that using infrared radiation as an energy source, the efficiency of enzyme pretreatment was significantly enhanced compared with conventional water bath assisted enzymatic pretreatment (p< 0.05), and the extraction rates of osthole and imperatorin by infrared-assisted extraction were significantly higher than those obtained with ultrasound-assisted extraction (p< 0.05). More importantly, the enzymatic pretreatment time was significantly shortened to 2 min of infrared assisted enzymatic pretreatment from 1 h of traditional water bath assisted enzymatic pretreatment. With the advantage of environment-friendliness, low cost, easy operation and high efficiency, the present enzyme pretreatment setup will find wide applications in enzyme pretreatment for natural product extraction in large scale.