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This paper introduces application of the GIS technology in the modern logistics information system, which has been designed based on the GIS technology. Design of this system use the object-oriented spatial data model and spatial databases based on the relational database to realize seamless integration of the data. The spatial data index uses the spatial data index structure based on improved R-Tree; The attribute data index uses the B+ tree construction of data; The network data transmission uses tri-stratification model, and developing with Java Applet or .net so as to cause memory, analysis and share of the magnanimous spatial data being possible. This system meet decentralized processing need of modern logistics enterprises enhanced the efficiency and the quality of large-scale logistics enterprise to set up the enterprise information system.