The low-carbon freight transportation system was introduced due to increase traffic congestion cost and carbon-dioxide for global climate change according to expanding city logistics demands. It is necessary to create 3D-based road network map for representing realistic road geometry with consideration of fuel consumption and carbon emissions. This study propose that 3D road network model expressed to realistic topography and road structure within trunk road for intercity freight through overlaying 2D-based transport-related thematic map and 1m-resolution DEM. The 3D-based road network map for the experimental road sections(Pyeongtaek harbor-Uiwang IC) was verified by GPS/INS survey and fuel consumption simulation. The results corresponded to effectively reflect realistic road geometry (RMSE=0.87m) except some complex structure such as overpass, and also actual fuel consumption. We expect that Green-based freight route planning and navigation system reflected on 3D geometry of complex road structure will be developed for effectively resolving energy and environmental problems.