According to the teaching philosophy of the outcome-based education, this study elaborates the development of a practical innovation course for biological engineering major after five runs of teaching practice and continuous improvement. It mainly includes the methods for selection of teaching subjects, implementation of teaching process, process assessment, evaluation and improvement. Based on the performance and achievements of three grades of students majored in bioengineering, we found that the logic and methods of the practical innovation course could greatly stimulate the motivation of students for learning, as well as their scores. Therefore, the logic and methods described in this study may serve as a reference for the reforms of practical training courses of engineering major under the background of Engineering Education Certification.