Abstract: Based on BSC's hierarchical objectives and key performance indicators evaluation, this article constructed a comprehensive budget management performance evaluation index system of universities with seven dimensions of performance, namely teaching, research, budget execution, finance, resource allocation, society and development. And a nonlinear model was established by using entropy method to determine the index weight, correcting index score based on the symbiosis and calculating evaluation values based on the synergism. The comprehensive budget management performance evaluation of a university in Beijing from 2009 to 2013 showed that the university has a comprehensive budget management to maintain a good level of performance. To be specific, the teaching dimension has the best performance, followed by the budget execution, whereas the financial performance is not so good.This result is basically consistent with the actual situation of the school. This showed that the established comprehensive budget management performance evaluation index system of universities is scientific and rational, with an objective and effective evaluation method, and true and reliable evaluation results; and the index system can be promoted for wide application so as to improve the overall comprehensive budget management performance of universities in China.