Objective To manage and use the medical knowledge resources effectively, we used the ontology to organize a medical knowledge base. This paper presented a building method for medical knowledge base. According to the approach, we established an ontological structure including Chinese traditional medical ontology and western medical ontology. Methods With the combination of the existent medical knowledge base, we applied NKI frame language to the system, and built the category of coronary heart disease(CHD) and other relevant categories. Based on the introduction of ontology theory, we utilized the Protégé 2000 of Stanford, the construction and maintenance tool of ontology,designed and completed medical knowledge base based on ontology. Results The medical knowledge base based on ontology was compared with the present medical knowledge base and it was indicated that the proposed system possessed the specialties of feasibility, extendibility and reusability. Conclusion The medical knowledge base based on ontology is supposed to be applied in some medical knowledge engineering fields.