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According to "Medium and long-term railway network plan" and railway "11 five-year plan", China will build 7,000 kilometers high-speed passenger transport special railway line. So railway ministry of China decided to develop High-speed Railway Decision Support System for helping high-speed railway construct and develop of China. On the basis of sufficiently analyzing the necessity and feasibility for using the multi-agent technology to develop the distributed high-speed railway intelligence decision support system, this paper proposes a three-layer structure of the IDSS for high-speed railway decision support (HSR-IDSS) based on multi-agent. HSR-IDSS has three-layer system structure, which includes client layer, decision logic layer and data service layer with distributed database, model base, knowledge base. The prototype application is implemented using Eclipse technology, and the agents are deployed on the FIPA-OS (Foundation for Intelligent Physical Agents-Open-Source) environment, we used J2EE (Java 2 Enterprise Edition) to develop the knowledge based of the agents' reasoning.