Training innovative professional degree postgraduate is the urgent requirement of national implementation of innovation-driven development strategy. Combined with the current situation of engineering innovation ability of professional master graduate students, this paper uses the survey data of innovation ability of professional degree graduate students and structural equation model (SEM)to study the influencing factors of innovation ability and the action mechanism of related factors from three dimensions.The research shows that the external conditions of innovation ability have the greatest weight among the influencing factors of innovation ability, teaching factors and tutor ability are important factors, the input of funds is positively related to the quality of training management process, professional practice environment conditions are positively related to the degree of achievement of innovation goals，the incentive policy has a direct positive impact on the supporting conditions for scientific research, the performance evaluation system and psychological drive are the important elements of the motivation of innovation. Hope to put forward some suggestions：increase investment in the cultivation of innovative ability of professional master postgraduates and raise funds for talent cultivation in a diversified way,Perfect the professional practice training system for professional master postgraduates, scientifically set up professional practice projects, and actively cultivate a good practice environment,establish a long-term mechanism and assessment policy for innovative practice, and to improve the evaluation, supervision and management system for the cultivation of innovative talents.