Economic responsibility auditing system of china is the emergence and development of audit supervision system to adapt to political and economic development. Evaluation of economic responsibility audit of economic responsibility audit is a very important part of economic responsibility audit evaluation index system is perfect, whether the results of the evaluation objective, fair and have a direct impact. In this paper, the characteristics of audit and evaluation index system of economic responsibility audit of University characteristics, from the University of level of economic responsibility audit to analyze the situation, to build the University of economic responsibility audit evaluation system of research by the University to set reasonable evaluation index system of economic responsibility audit, with a view to an objective reasonable evaluation of its economic responsibility.