Urban rainstorm waterlogging has become a typical “city disease” in China. It can result in a huge loss of social economy and personal property, accordingly hindering the sustainable development of a city. Impervious surface expansion, especially the irregular spatial pattern of impervious surfaces, derived from rapid urbanization processes has been proven to be one of the main influential factors behind urban waterlogging. Therefore, optimizing the spatial pattern of impervious surfaces through urban renewal is an effective channel through which to attenuate urban waterlogging risk for developed urban areas. However, the most important step for the optimization of the spatial pattern of impervious surfaces is to understand the mechanism of the impact of urbanization processes, especially the spatiotemporal pattern of impervious surfaces, on urban waterlogging. This research aims to elucidate the mechanism of urbanization’s impact on waterlogging by analysing the spatiotemporal characteristics and variance of urban waterlogging affected by urban impervious surfaces in a case study of Guangzhou in China. First, the study area was divided into runoff plots by means of the hydrologic analysis method, based on which the analysis of spatiotemporal variance was carried out. Then, due to the heterogeneity of urban impervious surface effects on waterlogging, a geographically weighted regression (GWR) model was utilized to assess the spatiotemporal variance of the impact of impervious surface expansion on urban rainstorm waterlogging during the period from the 1990s to the 2010s. The results reveal that urban rainstorm waterlogging significantly expanded in a dense and circular layer surrounding the city centre, similar to the impervious surface expansion affected by urbanization policies. Taking the urban runoff plot as the research unit, GWR has achieved a good modelling effect for urban storm waterlogging. The results show that the impervious surfaces in the runoff plots of the southeastern part of Yuexiu, the southern part of Tianhe and the western part of Haizhu, which have experienced major urban engineering construction, have the strongest correlation with urban rainstorm waterlogging. However, for different runoff plots, the impact of impervious surfaces on urban waterlogging is quite different, as there exist other influence factors in the various runoff plots, although the impervious surface is one of the main factors. This result means that urban renewal strategy to optimize the spatial pattern of impervious surfaces for urban rainstorm waterlogging prevention and control should be different for different runoff plots. The results of the GWR model analysis can provide useful information for urban renewal strategy-making.