The development of GIS technology has enabled the analysis of heavy rainfall vulnerability based on spatial analysis. In general, spatial analysis is performed based on property data and spatial data. Spatial data and attribute data differ in the generation units due to various reasons. The difference in these units can also cause problems in the results of the analysis. In particular, the Modifiable Areal Unit Problem (MAUP) that occurs according to the spatial unit setting is the most representative. The Modifiable Temporal Unit Problem (MTUP), which occurs according to the recent time unit setting, is also being raised. In this study, we analyzed the vulnerability of heavy rainfall in consideration of MAUP and MTUP. To analyze the effect of the MAUP, different administrative units were constructed and analyzed. In Seoul, Busan, and Ulsan, there was a scale effect in which disaster vulnerability was analyzed differently according to the analysis unit. In order to analyze the impact of MTUP, the range of study period was configured differently. The impact of the temporal boundary, in which overall disaster characteristics change and disaster vulnerability changes, has been identified. Analysis of regional disaster vulnerability considering MAUP and MTUP will be effective not only for the study of heavy rainfall disaster but also for setting the standard of disaster prevention policy.