Graduation design plays an important role in cultivating practical ability, innovation ability, and engineer quality of engineering undergraduates. At present, there is a decreasing trend in the graduation design quality of engineering students. Based on the practical work and full investigation, the main problems in the graduation design were analyzed. New measures for deepening the graduation design teaching reform were listed including starting graduation design earlier, quality monitoring of subject choosing, strengthening ability cultivation and process management, and strict grade assessing administration. The detailed analysis shows that these innovative teaching modes were feasible, which can make students systematically and comprehensively trained, increase students’ capability of analyzing and addressing practical engineering problems, and enhance the quality of graduation design effectively.