The emerging engineering education construction emphasizes the cultivation of students’ innovation ability. The course of civil engineering has strong theoretical and practical nature. This paper carries out the cultivation practice of students’ innovation ability under the concept of emerging engineering education combining with the long-span structure course. In the course teaching, we should emphasize the explanation and analysis of practical engineering cases, enhance students’ interest in learning engineering structure, and improve students’ ability to solve complex engineering problems; we should use online teaching resources to carry out research, optimize the course content, evaluate and guide students’ mastery of course knowledge points, and combine online teaching resources further broaden the knowledge of students; and project-based learning and science and education integration teaching are carried out, and project-based learning is used to provide students with structural design ability; science and education integration teaching is used to guide students to find, analyze and solve problems independently, and cultivate students’ innovation ability and scientific research ability. Through the reform of the above teaching methods, we can improve the teaching effect of the long-span structure course and promote the cultivation of students’ innovation ability.