In acupuncture research, the automatic selection of acupoints for treating stroke remains challenging. We design an ontology driven clinical decision support system to assist acupuncture treatment planning in the field of ischemic stroke and provide clinical decision-making services. This paper describes the development of a decision support system for the diagnosis and therapy of ischemic stroke based on clinical prior knowledge. An ontology is established in the field of acupuncture and ischemic stroke pertaining to clinical stages and their corresponding information components. Based on the ontology, the decision support system explores an acupuncture therapy for patient by considering therapy method, stimulation points and intensity, and manipulation ways with previous therapies. A performance analysis and assessment are proposed to evaluate the effectiveness of the decision support system. Experiments show that the proposed decision support system can aid ischemic stroke therapy decision-making by recommending the most relevant treatments suggestion through ontology inference. The visualization of diagnosis making and therapy planning also verifies the benefits of the combined exploration of decision support system and ontology, which promotes the development of acupuncture from individualized empirical knowledge to large-scale evidence-based medicine.