The course of Separation Engineering Experiment is an important undergraduate practical course for natural science majors such as pharmacy, agriculture, biology and food science. Taking the biopharmaceutical specialty of Jilin Institute of Chemical Technology as an example, through adding independent design experiment, reasonable adjustment of experiment and production practice program, increasing the proportion of comprehensive experiment, and paying attention to experiment principle and process estimation, students can become active instead of passive in doing experiment, so as to make connection with the next stage of study or work after graduation.