In view of insufficient attention paid to scale effects and the interaction of multiple factors in urban waterlogging research, especially the significant limitations in mountainous cities with strong spatial heterogeneity, taking the central urban area of Chongqing City as the study area, the spatial analysis method was used to identify the spatial distribution of waterlogging sites at different scales based on the waterlogging site data from 2015 to 2021. Combined with the statistical analysis method, correlations between each factor and the spatial distribution of waterlogging sites at different scales, as well as the changing trends of the independent and interative effects of each factor on the spatial distribution of waterlogging sites were explored.The results show that spatial distribution of waterlogging sites in the central urban area of Chongqing City remains stable at all scales.The spatial aggregation feature is most obvious at 5 km scale, while the effect and mechanism of the same factor show obvious differences at different scales for different urban characteristics.