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This paper introduces the concept and the classification of Web mining, analyzes the Web mining process and the analysis techniques often used. We propose the system architecture based on Web mining of E-commerce application, and discuss the analysis model of Web Mining and the applications in E-commerce. Web mining can find potential customers and achieve website structure optimization. It can provide customers with personalized service, realize business intelligence and Web use describing, and has certain promoter action to the network security. It has important directive significance for the development of E-commerce to study the E-commerce application based on Web mining.