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Because of the limitation of intrusion detection systems (IDS), developing IDS based on mobile agent become a hotspot. Beginning with discussing the defects of traditional IDS, and analyzing the advantage of operating with mobile agent in IDS, this paper presents a multi-layer IDS model based on mobile agent, and then discusses the operation process and implementation of these IDS. These model implements special functions via mobile agents traveling in every layer, which can minimize the cost, and defense attacks effectively from insider or outsider. At the same time, enhance the ability of rapid response, easy configuration, flexibility, retractility, etc.