This paper proposes a new solution to introduce ideology content into the teaching of engineering major courses to accommodate recent Ministry of Education requirements of university courses. Based on our teaching of the optional course “Modern Microscopy: Instrumentation and Biomedical Applications” for undergraduate students in the School of Biomedical Engineering, Shanghai Jiao Tong University, we developed methods to integrate the three ideological elements of scientific spirit, engineering ethics and practical ability to produce an effective problem-based learning program, with both online and offline mixed teaching. Taking the student-centered, teacher-led and outcome oriented education model, we guided students to actively participate in knowledge-based learning, discussion and practical training during the whole process of teaching activities, and achieved the expected results. We suggest that our experience can serve as an effective reference and guide in the implementation of ideological content of the same type in other engineering professional courses.