Assessing the innovative potential of graduate students has an important impact on China’s construction of innovative nation. To assess the innovative capabilities of engineering graduate students, this article firstly constructs an evaluation index system through literature analysis, expert opinion consultation and other methods from the six aspects of personal thinking, theoretical basic teaching, multi-disciplinary intersection, scientific research support conditions, social practice ability and mentor education mechanism. Secondly, a comprehensive assessment model for the innovation capabilities of engineering graduate students is developed through two evaluation methods, namely the TOPSIS method and the comprehensive index method. A comprehensive assessment is conducted to a sample of 24 graduate students specializing in engineering management within the civil engineering program at the School of Civil Engineering and Architecture, East China Jiaotong University. The evaluation outcomes of the two evaluation methods are basically the same, underscoring their capacity to impartially depict the innovation capabilities of engineering graduate students. The primary factors currently influencing the innovative capabilities of new engineering graduate students are their individual thought processes and personality traits, mentoring mechanism, and social practice ability. Therefore, corresponding measures should be taken to cultivate their innovation interests, formulate reasonable training plans, and vigorously support practical activities, so as to boost the innovative skills of graduate students in new engineering programs.