Although Chinese medicine treatments have become popular recently, the complicated Chinese medical knowledge has made it difficult to be applied in computer-aided diagnostics. The ability to model and use the knowledge becomes an important issue. In this paper, we define the diagnosis in Traditional Chinese Medicine (TCM) as discovering the fuzzy relations between symptoms and syndromes. An Ontology-oriented Diagnosis System (ODS) is created to address the knowledge-based diagnosis based on a well-defined ontology of syndromes. The ontology transforms the implicit relationships among syndromes into a machine-interpretable model. The clinical data used for feature selection is collected from a national TCM research institute in China, which serves as a training source for syndrome differentiation. The ODS analyzes the clinical cases to obtain a statistical mapping relation between each syndrome and associated symptom set, before rechecking the completeness of related symptoms via ontology refinement. Our diagnostic system provides an online web interface to interact with users, so that users can perform self-diagnosis. We tested 12 common clinical cases on the diagnosis system, and it turned out that, given the agree metric, the system achieved better diagnostic accuracy compared to nonontology method-92% of the results fit perfectly with the experts' expectations.