To solve the logistics information system based on GIS application problems of small and medium-sized logistics enterprises, the software architecture of the traditional logistics information system and system based on GIS technology is analyzed, and their advantages and defects are pointed out. On this basis, a kind of service oriented four layers logistics system architecture based on components GIS is designed, using ArcSDE and ArcIMS as GIS platform, the detailed deployment of the architecture are given. The relationships between the infrastructure layer, the spatial information support layer, the service support layer, the business application layer and the components are Expounded. The architecture features of business agility, loose coupling of system interface, combine and reusability of functional components are verified by its prototype system.