Fermentation Engineering Experiment is one of the important engineering courses for bioengineering majors. It is also an important course to train students’ engineering design, engineering practice and innovative thinking. Based on conceive-design-implement-operate (CDIO) engineering education model, Fermentation Engineering Experiment carries out curriculum design and goal-oriented teaching mode reform by constructing modular curriculum content and project-oriented system of conception, design, realization and operation. The fermentation engineering experiment course as a carrier, it integrates engineering basic knowledge, fermentation engineering system practical ability, team cooperation ability and innovation ability training. The evaluation system of students’ learning effect based on outcome-based education (OBE) concept was established, and the teaching task of Fermentation Engineering Experiment course was finished. The students’ satisfactions for the reforming course of Fermentation Engineering Experiment have improved, and the teaching effect is remarkable.