In order to improve the innovation ability training level of civil engineering graduate students, the following seven factors affecting the cultivation of innovation ability of graduate students were analyzed: source of students, academic dissertations, supervisors, training environment, training model, training system and large-scale engineering. And the inner law of the interactive development between the seven key factors was revealed. The reform of educational idea, teaching method and mean were carried out. Four training platforms were established, including the comprehensive experiment and training platform inside school, the sharing training platform inside and outside school, the innovation alliance training platform and the large-scale engineering industrial base training platform. Three training models were proposed based on large-scale engineering, including the practical research and development mode, the group discussion mode and the open training mode. Finally an innovative three-dimensional training system integrating “production, study, research and application” was created. These innovations have been put into practice and achieved remarkable effects. The teamwork-oriented, engineering practice and innovation ability of graduate students were greatly improved.