To implement the “synergistic development of five educations” and address the existing issues in the current comprehensive quality evaluation system for medical postgraduate students (original system), this article constructs a new comprehensive quality evaluation system (new system) from a multidimensional collaborative perspective. Through the trinity framework of “basic evaluation, incentive evaluation, and negative list”, it explores the application effects of the new system in assessing the comprehensive quality evaluation of medical graduate students. The research shows that the operational efficiency of the new system has significantly improved, outperforming the original system in terms of student participation rates, evaluation effectiveness, and feedback rates. This article summarizes the experience of the evaluation system reform and proposes future prospects, offering valuable insights for the reform of medical education evaluation.