Engineering education undertakes the mission of cultivating engineering talents, and project-based teaching has played an important role in cultivating students' engineering and technology ability. However, for the cultivation of composite talents in new engineering disciplines, project-based teaching still focuses more on the practical application of students' professional knowledge, and there are serious constraints such as the lack of engineering thinking and overloaded professional knowledge boundary. Therefore, it is essential to develop a project-based deep teaching model within the framework of systems engineering, establish a cross-disciplinary talent cultivation pathway, delve into the profound implications of systemic thinking inherent in comprehensive literacy, and devise multi-dimensional, multi-perspective, deep-level teaching strategies to cultivate students' higher-order thinking abilities and enhance their overall literacy.