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Regular security assessment should be one of the major steps for every e-commerce system to minimize the number and impact of security breaches. This paper proposes a new assessment model for e-commerce. First of all, we construct a three level assessment architecture based on fuzzy comprehensive judgment of E-commerce. Secondly, entropy weight coefficient is applied to overcome the subjectivity and data redundancy. Finally, the effectiveness of the proposed model is demonstrated with a case study in an actual e-commerce system. In practice, this model can be employed for assessing security degree of e-commerce system, and identify security threats. And it can effectively guide the implementation of security plans and countermeasure selections.