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Flooding is the most pervasive hydrological disaster globally. This study presents a comprehensive analysis of torrential rain and flood characteristics across three major urban agglomerations (CY, MRYR, and YRD) in the Yangtze River Basin from 1991 to 2020. Utilizing satellite-derived microwave SSM/I data and CHIRPS precipitation datasets, this study examines the impacts of urbanization and climate change on flood risk patterns. The results showed: (1) In 1998, the MRYR had the highest flood risk due to heavy rainfall and poor flood control, but by 2020, risk shifted to the CY with rapid urbanization and more rainfall, while the YRD maintained the lowest risk due to advanced flood control. (2) The relationship between impervious surface area and flood risk varied by region. The CY showed a negative correlation (−0.41), suggesting effective flood mitigation through topography and infrastructure; the MRYR had a slight positive correlation (0.12), indicating increased risks from urban expansion; and the YRD’s weak negative correlation (−0.18) reflected strong flood control systems. This research underscores the imperative of strategic urban planning and effective water resource management to mitigate future flood risks and contributes valuable insights to ongoing efforts in flood disaster prevention and control within the Yangtze River Basin.