Using virtual simulation technology and the GaeaExplorer 3DGIS platform, the 3D visual and analysis system of lightning data is designed and developed, which constructs the spatial database and the 3D simulate scene and realizes the fine 3D visualization of lightning data for the first time. By means of the spatial analysis capability of GIS, this system develops the function of data management and spatial analysis. It is important for lightning risk reduction and decision service to provide 3D data. The result shows that the system can provide a good application experience and make a solid foundation for lightning detection and scientific researches.