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In this paper, after the introduction of ontology-based domain knowledge bases and domain knowledge representation, a formal query model of intelligent search agents that can search over distributed knowledge bases with heterogeneity for Web-based intelligent tutoring systems is proposed; and the searching process of these agents is analyzed. Ontologies are introduced to describe the semantic information of knowledge bases in order to express fully the semantics of queries in our Web-based intelligent tutoring system. This model improves the relevance of the searching results. At the same time, it reflects the dynamic change of the information in the knowledge bases and reduces the consistency and efficiency problem caused by using globe ontology.