Based on the sample of A-share listed companies in Shanghai and Shenzhen Stock Exchanges from 2010 to 2013 implementing internal control evaluation, using random effect Logistic model, this paper discusses the impact of internal control evaluation on audit opinion deviation.. The result shows that after internal control evaluation and audit, enterprises with higher evaluation has less probability of audit opinion deviation. Further research shows the implementation of internal control evaluation procedures will strengthen the trend of reducing audit opinion deviation owing to the original audit resources input and reduce the trend of increasing the audit opinion deviation resulted from the environmental uncertainty. The evaluation of internal control by the firm has measured the environment of the enterprise to report the true situation, which reduces the deviation of the audit opinion, and reduces the probability of the audit opinion deviation through the “spillover effect” of the business resources and the “complementary effect” of the cognitive resources.