In the current higher education landscape, universities are facing expanding requirements beyond teaching and research. Evaluation methods must evolve accordingly to prevent universities from facing development dilemmas. Current mainstream evaluation methods primarily emphasize the research domain, often failing to holistically capture a university's overall performance and multifaceted contributions. From the functional perspective, this study views the university as a parallel input-output model consisting of separate subsystems. The proposed model demonstrates that a unique solution can be identified when assessing different functions, and it offers a cross-efficiency algorithm based on evidential-reasoning that can integrate peer evaluation. Utilizing data from 94 high-level universities in China, the proposed model exhibits improvement over alternatives. The analysis encompasses short- and long-term perspectives, subsystem and overall system viewpoints, and cross-year comparisons, while exploring dimensions like regional location, school type, and policy support. Lastly, this study analyzes China's current policy situation and provides relevant recommendations based on the research findings.