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With the developing of spatial information and Internet technology, marine management departments begin to design and develop information systems on the basis of GIS technology. It helps government to improve their work efficiency. However different departments use different technologies, different data formats and different work flows, and one department can not access other departments' data or use their functions. It causes information island and resource waste. In order to solve these problems, this paper studies the coupling relation between Web service and GIS technology, and designs the multi-level architecture of China Digital Ocean Information System based on SOA (service-based architecture), and discusses various application modes for users at different levels. At last, the architecture and application modes proposed in this paper are verified by implementation of China Digital Ocean Prototype System.