The semantic web is taken as next generation standards of information exchange on the internet to overcome the limitations of the current web. To utilize the information on the semantic web, tools are required the functionality of query search and reasoning for the ontology. However, most of semantic web management tools cannot efficiently support the search for the complex query because they apply Triple-based storage structure about RDF metadata. We design the storage structure of the ontology in corresponding with the structure of ontology data and develop the search system(SMART-DLTriple) to support complex query search efficiently in this research. The performance of the system using new storage structure is evaluated to compare with the popular semantic web management systems. The proposed method and system make a contribution to enhancement of a practical ontology reasoning systems due to improved performance of the ontology search.