We in this paper proposed a distinction method to compare objects in the Korean medicine ontology. Comparing same and different information between two objects, two scenarios to use our system were designed and implemented. One is the distinction of formulas, medicinal materials, and acupuncture points and the other is the distinction of effects, treatments, and symptoms. To compare objects easily, the decomposition of effects and treatments and the processing of medicinal materials were provided. Also, information of each object was shown through the link to the semantic search system. Our distinction method and system could be helpful to compare and distinct two objects in the diagnosis systems or search systems of Korean medicine information.