Abstract: In the construction of a clean government at universities, the economic responsibility audit is helpful to the practice of the thought of “Three Representations”, enhancement of management and supervision of cadres, and prevention of the corruption in universities from the source. However, the inadequate value on the audit results, single ways of expression, confinement of employment, low quality of audit, and lack of unified evaluation systems of audit, all these have led to the fact that such kind of audit only becomes a formality. The measures to strengthen the employment of economic responsibility audit and the construction of a clean and honest government include the exertion of the function of audit which helps to start from supervision and find the clue of corruption, construction of relevant system which can prevent the corruption from the source, and organization of relevant forces to control the corrupted behaviors of cadres