Abstract: In view of the large number of valuable Web information that has not been used existing in the network, by constructing ontology the deep Web information can be described to achieve the purpose of retrieval and utilization and sharing. Based on the analysis of the Mongolian features, challenges of information processing, and the current research results, this paper proposes an automatically Mongolian ontology building method based on relational database, and designs Mongolian logistics automatically building ontology and reasoning query system taking logistics data in Inner Mongolia as an example.First, the obtained ontology is instantiated by the prototype system, and it is also verified on the help of Jena reasoning subsystem. The consistency and reasoning ability of the obtained Ontology were verified.Finally, this prototype system was applied to the decision-making process in the field of logistics business in Inner Mongolia.