The Pearl River Delta (PRD) is one of the three urban agglomerations in China that have experienced rapid development. For this study, a core area of the PRD was identified, comprising the highly urbanized areas of Guangzhou, Foshan, Zhongshan, Zhuhai, Shenzhen, and Dongguan Cities. The expansion of these urban areas was tracked across three time periods—the year population urbanization rate exceeded 70% (2000), 18 years before (1982), and 18 years after (2018). This study used the Weather Research and Forecasting (WRF) model to explore summer rainfall changes across different urbanization periods in the PRD core area. The results show that urban land expansion mainly occurred in the post urbanization period. Rainfall changes across different urbanization periods were roughly consistent with previously observed spatial and temporal changes accompanying urban expansion in the PRD core area. Extreme rainfall mainly increased in the post urbanization period, shifting rainstorm center towards the PRD core area. Further causal analysis revealed that land use changes affected rainfall by altering thermodynamics and water vapor transfer. The urban expansion changed the surface energy balance, resulting in increased surface heating and heat island effects. The heat island effects thickened the planetary boundary layer and increased vertical wind speeds, which initiated dry island effects, thereby causing more water vapor transportation to the atmosphere. Consequently, rainstorms and extreme rainfall events have become concentrated in urban areas.