Aiming at improving the level of refined design of geotechnical investigation of water transportation engineering，the research of development and application of geological 3D design system based on BIM technology in water transportation engineering is carried out. MR-GEO system based on MicroStation platform with the professional toolset and resource database is developed，which realizes the processing of interface data，generation of the 3D geological model with geotechnical information，drawing output，calculation，and analysis of results and other main functions. With the application in the project case，the system gets verified，which provides a reference for similar engineering requirements.