From the respects of disastercausing factors, disasterbreeding environment and disaster bearing body, the article studies disaster risk assessment and zoning methods, according to the natural disaster system theory and the natural disaster risk assessment theory, taking Sanming of Fujian as an example, by use of meteorological data and geographic information data, social economic development scale, population density, land use status and lightning disaster data, by means of the statistical method and disaster analysis, questionnaires and other methods to establish the quantitative relationship between evaluation index and risk assessment and GIS technology to overlay the vulnerability elements. Then on the platform of GIS, all the data are put into the 1 km×1 km grids, processed and quantized and then the vulnerability of lightning disaster risk zoning map and the fine zonation model of lightning disaster vulnerability are gained based on the GIS overlay method. This system has good application potentials for the development of lightning protection and disaster reduction capability of meteorological public services and is of great significance to carry out monitoring, early lightning warning and forecast, and lightning protection and disaster reduction researches.