In order to address the urgent need to deal with the problem of urban waterlogging disaster in urban governance in the Pearl River Delta (PRD) region, on the basis of constructing an indicator system for assessing the resilience of urban waterlogging disaster, the spatial distribution, dimensional differences and heterogeneity of the waterlogging disaster resilience of the PRD urban agglomeration in 2022 are measured and analyzed using the CRITIC-TOPSIS combination model and the resilience development degree, and the obstacle model is adopted to identify the obstacle factors. The results show that the spatial distribution of waterlogging resilience in the PRD region decreases from Guangzhou and Shenzhen to the surrounding area, presenting the characteristics of “High in the center, low around the perimeter”. The development of each city in the dimensions of economy, society, ecology, infrastructure and population is significantly different. In the categories of resistance, adaptability and recovery to waterlogging disaster, Guangzhou and Shenzhen have the characteristics of “overall excellence”, and the development trend of the region is “echelon”. In addition, economic development is the primary obstacle to the improvement of the resilience of waterlogging disasters in Huizhou, Jiangmen and Zhaoqing, social life is the primary obstacle to the improvement of the resilience of waterlogging disasters in Foshan, Dongguan and Zhongshan, and ecological environment is the primary obstacle to the improvement of the resilience of waterlogging disasters in Guangzhou and Zhuhai.