Study the concept of similarity is the basis to achieve semantic interoperability in the Semantic Grid，but also knowledge representation and information retrieval in an important research content. In this paper, the ISA hierarchy ontology relationship, considering the degree of semantic overlap, semantic distance, level, depth, level, based on the gradient to other factors, presents a conceptual ontology similarity calculation. Experimental results show that the method and the method and the subjective judgments compared to traditional computing methods to improve the accuracy of computer similarity.