Abstract: Under the background of realizing the independent control of key core technologies, and in order to cultivate students’ system engineering thinking, and then the innovative and interdisciplinary talents, the paper puts forward a new multi-level integrated teaching mode, that is, the integration and interconnection of undergraduates and postgraduates, the integration and interaction of theory and practice, and the integration and systematization of online and offline teaching and learning. In addition, the paper explores the relevance of the courses’ contents, and builds an online virtual simulation cloud platform and an offline instrument operation experiment platform. Meanwhile, in the multi-level integrated teaching mode, the curriculum-based ideological and political education are strengthened, and diversified ways of assessment are adopted. The practice shows that the multi-level integrated teaching mode can not only improve the quality of the teaching of the courses and arouses students’ enthusiasm for learning, but also help to cultivate students’ system engineering thinking, so that they can understand things from the overall perspective and be able to find, raise and solve problems.