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Component based development technique is often used to develop various complex software systems, especially in e-commerce system, due to its flexibility and efficiency. But such a system must provide a mechanism with which developers can easily manipulate the underlying structures to meet the application requirements, in particular in the real time and safety properties. This paper proposes a new method for formally modeling the component based e-commerce system using hierarchical timed automata, which use hierarchical structures to organize the design schemes in different levels of an e-commerce system. In addition, we analyze the modeling process of a micropayment system as a case. Compared with previous works, our approach can formally model the e-commerce system in a hierarchical and uniform framework.