The invention discloses a semantic data query system with optimized storage, comprising a semantic data importing module, a semantic data storage management module, a stored data persistence module and a semantic data query module. The system supports import of various regularly described resource description framework data, and can map a storage model to a magnetic disc, thereby implementing quick reproduction of an internal memory storage model. In the system, a query graph model operable to a bottom-layer storage model is formed by transforming and processing the semantic data query; a cost model for querying connection operations is established by counting bottom-layer stored data, and an optimization module for the semantic data query is implemented through a greedy algorithm; and sequence of query is regulated, so that query performance is improved.