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The complexity of information system architecture is a key factor which impresses the development of information system. Firstly, the features of systems interface description are analyzed, which is a product of system view of DoD Architecture Framework, then based on the product of systems interface description, the fundamental models of systems and interfaces are established. According to the basic structure of systems and interfaces, the entropy-based complexity analysis method on architecture of information system is provided in the paper. Finally, a concrete example is given to expatiate on the method.