Web-based GIS provides interactive mapping and spatial analysis capabilities for enhancing public participation and collaboration in decision-making processes. This paper proposed a system design for a Web-GIS based collaborative transportation planning system. The system aims to offer a new efficient means for transportation planning and to enable different departments and public to participate the activities of urban transportation planning, such as geo-referenced information collection, so that transportation department planners and public could work together to fulfill the planning work. The system has adopted three layers system infrastructure of J2EE. The database included the geography data, transportation planning projects data and CSCW data. The system adopts Java GIS applet to communicate with database and EJB. The geographical interface is shown with a Java GIS applet in the Webpage. The system infrastructure design has been experimented in a prototype system. It can be applied to the transportation-planning field for transportation information broadcasting, data management, statistical analysis, and collaborative decision-making.