With the appearance of the new engineering concept in 2017, the mode of talents development in colleges and universities has also changed. And the new engineering talents need to be more practical and innovative abilities. However, the professional certification of engineering education is an important guidance for the teaching of engineering majors in China, and it is the core idea of output-oriented, student-centered and continuous improvement to construct the quality control system of engineering education in colleges and universities in China. Combining with the core idea of engineering certification and the new requirements under the background of new engineering, in this paper, we put forward to a set of comprehensive software engineering course design for engineering certification in the new engineering environment, which is guided by engineering education, aims at improving students' engineering practical ability and innovation, provides a method of solution for the reform of software engineering course design under the new engineering background.