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The safety assessment index system is established on the elements of mobile payment system and hierarchical structure of software risk assessment. In order to make up for the deficiencies of traditional risk methods and adapt to fuzzy description in mobile payment system, the hierarchical safety assessment model is developed with the extension theory as the core. The extension method converts the multi-object assessment to single object assessment by combining qualitative and quantitative analysis to achieve a comprehensive assessment state. The case studies show that this assessment model adapts to the actual situation of mobile payment system, and is scientific and effective which can provide dependable evidences for safety management.