Graduation design is not only the most important comprehensive practical teaching component for civil engineering majors at the undergraduate education stage, but also one of the primary phases for training excellent engineers. Several classic problems about the graduation design currently exist in application-oriented institutes. Based on the “excellent engineer training program” established by the Ministry of Education, the teaching reform of graduation design was studied in the following aspects: the topic selection, the teaching method optimization, the innovation system establishment, the teachers’ ability improvement, the management appraisal system and the safe concept of civil engineering. Favorable results have been obtained, which can provide a reference for the revision of graduation design guides aiming at training excellent engineers.