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In view of uncertainty of comprehensive evaluation index of security risks investigation and govern ability of coal mine, a set pair analysis and evaluation model was established. The model determines evaluation index system from two aspects of personnel factors and govern factors, taking positive and negative, similarity and dissimilarity connection degree into account to obtain a comprehensive connection degree, so as to realize quantitative evaluation of security risks investigation and govern ability of coal mine. The result of case analysis shows that the proposed model can reasonably evaluate security risks investigation and govern ability of coal mine, and the result is in line with the actual situation.