Checking the structural integrity efficiently is one of the research hotspots in the field of MOF(meta object facility) repository system consistency. In this paper, we propose an efficient and automatic approach for checking the structural integrity by means of description logics. Firstly, according to the characteristics of MOF architecture, we study how to transform different levels of metadata into SROIQ(D) knowledge base. Then we study how to extract metadata to improve the efficiency of the checking process. We propose the concept of logically independent fragment of metadata. By extracting property deductive fragment and classification deductive fragment respectively, we present the algorithm to generate the minimum logically independent fragment. Since this kind of fragment is the closure of logical implication for a given metadata element, all relevant information about the given metadata element is completely preserved, thus the checking process can be performed on a smaller set of metadata rather than on the entire repository. Finally, we study how to perform checking based on logically independent fragment. The experimental results show that the average size of the metadata fragment generated by our approach is significantly smaller than its original size, and the efficiency improvement of the checking on the metadata fragment ranges from 1.47 times to 3.31 times. The time performance comparison with the related approaches also shows the effectiveness of our approach.