In order to improve display effect and analysis and decision ability of marine geology information, the Marine Geology 3D Geographic Information System is established based on Skyline software and Visual studio.NET development platform. It is a WebGIS application platform, builds submarine 3D scene by using the satellite image and marine geology survey data, provides 3D scene roaming, attribute query, submarine terrain browsing, sea level rise simulation, coastline change simulation, mineral resources evaluation and other functions, provides service for marine geology survey, development, management, and decision making. This paper mainly introduces the design of system framework, data preparation, and function realization for the purpose of discussing the design and realization of 3D WebGIS based on Skyline.