In the traditional application-oriented training of civil engineering professionals, the graduates are required to have solid professional skills and rigorous, conservative and accurate thinking habits. In the new era, the transformation needs of civil engineering industry put forward higher and higher requirements for graduates' innovative thinking ability. Thinking is the premise of innovation, and high-quality thinking is the basis of innovation achievements. Civil engineering students generally have strong thinking patterns and are difficult to recognize their own weaknesses. Improving their thinking habits is very important to improve their innovative ability. Based on the teaching practice of civil engineering innovation course offered by our university, this paper analyses the needs of innovative ability, explores the thinking characteristics of civil engineering students, and expounds the necessity of offering innovative thinking and innovative ability training courses. Combining with the teaching practice, the composition and significance of the teaching content of the course are explained and discussed.