Along with the demand of our country on cultivating scientific and innovative talents, we are encouraged to reform traditional experiment teaching content by focusing on the country’s development needs and introducing frontier science to the designation of comprehensive experiment. Taking the multidisciplinary characteristics of biomedical engineering into account, we innovatively design a research-based comprehensive experiment, that is functional magnetic composite nanomaterials for enrichment of phosphopeptides. This experiment, which covers chemistry, materials, biomedical and other disciplines, exhibits great application prospect and scalability, and leaves the student with abundant research space for further exploration and development. This experiment integrating multiple disciplines not only develops the innovative thinking of students, but also enhances the research ability for potential scientific and innovative talents.