Course design is a very important practical teaching in the process of civil engineering professional training. Based on the existing teaching experience of professional curriculum design, combines the characteristics of our civil engineering major, this paper analyzes the problems of curriculum design in civil engineering major, and puts forward the reform initiatives of throughcourse curriculum design in civil engineering based on engineering education certification and project coherence, in order to solve the drawbacks of traditional teaching mode of curriculum design, help students to solve complex engineering problems in a multidisciplinary environment, and highlight the cultivation of students’ engineering practice ability and innovative comprehensive ability under the background of engineering certification, so as to better serve the goal of building first-class civil engineering major and nurturing first-class civil engineering talents.