With the application of e-government becomes more and more extensive, the security issues become increasingly important. The paper firstly presents a relatively complete e-government security risk evaluation index system basing on comprehensive analysis of risk factors which affects e-government security. Then we conduct orthogonal transformation to the indexes for eliminating duplication between them. After that, we combine entropy weight coefficient method and AHP to determine the weight of risk factor index, and the improved D_S evidence theory is introduced to deal with the uncertainty in risk assessment. Finally, an example is cited to verify the validity of this method, compared with the result of fuzzy comprehensive evaluation, we can see the effectiveness of this method in e-government security risk assessment.