With the development of the Semantic Web, the interoperability and sharing of expert system were put forward more advanced requests. The researches for new knowledge representation and knowledge base systems are important trend. As a formal, explicit specification of a shared conceptualization, ontologies provide frames for interoperability between different systems and can solve the sharing and interoperability problem effectively. There were a variety of doubts in some beginners’ mind with the concepts of knowledge base, ontology and expert system. Based on the author's understanding and practice, the systematic comparative analysis between knowledge base, ontology and expert system in the domain of knowledge engineering were proposed in this paper, in order to make these terms less confused and more clearly comprehensible.