This study identified a lackluster classroom atmosphere in advanced biochemistry, characterized by low levels of active student participation in interactive communication and subpar quality of after-class learning tasks. The issues stemmed not only from students' learning attitudes, such as insufficient attention to the curriculum, but also from the course's inherent lack of challenge. Employing flow theory, we optimized teaching content, enhanced course difficulty, reformed assessment methods, and incorporated information-based teaching tools to redesign the instructional process. Through a questionnaire survey, students evaluated teaching effectiveness after implementation of the changes: a majority expressed satisfaction with the moderate difficulty of the course and enjoyment of the classroom instruction, and reported experiencing positive emotional flow. Peer experts commended the course, noting its lively atmosphere and the students' acquisition of both basic research methods and foundational knowledge. The findings will be used to continually enhance graduate students' innovation abilities and sense of achievement through ongoing reforms.