In recent years, the frequency and scale of the natural disasters are growing rapidly due to the global climate change. In case of the urban flooding, high-density of population and infrastructure has caused the more intensive damages. In this study, we analyzed the spatial characteristics of urban flooding damage factors using GWR(Geographically Weighted Regression) for effective disaster prevention and then, classified the causes of the flood damage by spatial characteristics. The damage factors applied consists of natural variables such as the poor drainage area, the distance from the river, elevation and slope, and anthropogenic variables such as the impervious surface area, urbanized area, and infrastructure area, which are selected by literature review. This study carried out the comparative analysis between OLS(Ordinary Least Square) and GWR model for identifying spatial non-stationarity and spatial autocorrelation, and in the results, GWR model has higher explanation power than OLS model. As a result, it appears that there are some differences between each of the flood damage areas depending on the variables. We conclude that the establishment of disaster prevention plan for urban flooding area should reflect the spatial characteristics of the damaged areas. This study provides an improved understandings of the causes of urban flood damages, which can be diverse according to their own spatial characteristics.