With the development of national strategy, higher requirements have been put forward towards the cultivation mode in Biomedical Engineering (BME), an emerging interdisciplinary subject. Since the existing training mode was inefficient in achieving educational objectives, innovational reformation is of urgent need. In this paper, commonly existing problems in graduate cultivation in BME among colleges and universities are analyzed in detail. A case study of graduate education reformation in Shanghai Jiao Tong University Biomedical Engineering major was conducted. Taking the Biomedical Engineering Major of Shanghai Jiao Tong University as an example, a series of reform measures were implemented including an adjustment in curriculum system and an increase in medical courses and practical education, and further development considerations were put forward. In this way, we hope that the quality of teaching together with the talent training system of BME in China will be improved in order to boost graduate students’ comprehensive capabilities both in the integration of medicine-engineering and in the practice of industry-academia-research and finally to benefit people’s health.