Training innovative postgraduate with professional degree is the urgent requirement of national implementation of innovation-driven development strategy. Comparing with academic degree graduate students, they have no obvious advantage in engineering-innovation ability. Instead, they are weak in basic knowledge and R&D ability. Through literature reading research and expert interview, this paper studies the factors that influence the innovation of professional degree graduate students from 15 items,and designs questionnaire. Factor analysis is used to identify the key factors according to the questionnaire。Some suggestions are put forward to improve innovation ability of professional degree graduate students:improving the system of organization and talent security, building innovative training platform, carrying out funds safeguard, establishing long-term effective mechanism of innovation practice and supporting policies, and strengthening talent training evaluation and supervision management.