XML is increasingly important in data exchange and information management. Starting point for retrieving the structure and integrating the documents efficiently is clustering the documents that have similar structure. The reason is that we can retrieve the documents more flexible and faster than the method treating the whole documents that have different structure. Therefore, in this paper, we propose the similar structure-based incremental clustering method useful for retrieving the structure of XML documents and integrating them. As a novel method, we use a clustering algorithm for transactional data that facilitates the large number of data, which is quite different from the existing methods that measure the similarity between documents, using vector. We first extract the representative structures of XML documents using sequential pattern algorithm, and then we perform the similar structure based document clustering, assuming that the document as a transaction, the representative structure of the document as the items of the transaction. In addition, we define the cluster cohesion and inter-cluster similarity, and analyze the efficiency of the Proposed method through comparing with the existing method by experiments.