In view of the problem of lacking interoperability in the process of security domain division, this paper presents a new method for the division of the Egovernment system. There establishes three level index system of asset classification and an assets value similarity index system of the egovernment system based on the similarity value of the assets, and uses a fuzzy clustering method and Matlab to divide the security domain in a particular egovernment system based on the three levels index system of asset classification and the assets value similarity index system of egovernment system.