A novel reduction method of high dimensions based on artificial neural network was proposed for the effect reduction of Chinese traditional medicine prescription. Based on the similarity information between properties, it created a property distance matrix.The matrix was loaded into an artificial neural network, and through training the artificial neural network, it got the reduce result of high dimensions. Based on the new method, a prescription analyze system of Chinese traditional medicine was implemented. The efficiency of the new method was proved by experiments in effect reduction of Chinese traditional medicine.