Case retrieval is a key process of Case-based Reasoning (CBR) system, and it is also one of hot research field of artificial intelligence. The calculation method of case similarity is the key technology of case retrieval. The set pair analysis(SPA) is applied to calculate the similarity of two sets between the target case and source case of case base, and the case retrieval model is built by the property and contact degree. The problem of multi-word synonyms is solved by the semantic extension of ontology, so the accuracy of the retrieval uncertainty is improved effectively. Experimental results on Asthma diagnosis show that ontology based on set pair analysis case retrieval model not only reduces the amount of computation, but also improve the recall and precision. All this provides technical basis for medicine diagnosis and treatment the next step.