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We consider the problem of constructing special knowledge-base to integrate a large number of interface schemas over the Deep Web. The scale of the problem and the diversity of the sources present serious challenges to the conventional manual or statistics-based approaches to schema integration. Domain knowledge-base construction plays an important role to it. The paper discusses knowledge representation, knowledge storage and its construction for three real-world domains based on database schemas, Web query interfaces and traditional methods of Knowledge construction. The architecture is a semantic network constituted by many kinds of knowledge units. Applications of the Deep Web query interface mapping and intelligent user query intension recognition based on our domain knowledge-base are also introduced briefly. Extensive experiments are conducted and results show that our approach is effective. The research provides a basic resource construction technique for semantic Web information processing. It is valuable to large scale applications of intelligent Deep Web integration and information retrieval.