In the context of global climate change and rapid urbanization, the risk of urban waterlogging is one of the main climate risks faced by the Beijing-Tianjin-Hebei (BTH) urban agglomeration. In this study, we obtain the urban waterlogging risk index of the BTH urban agglomeration and assess waterlogging risks in the built-up area of the BTH for two time periods (1961–1990 and 1991–2019). We analyze the economic and social data as well as the climate data from 149 meteorological observation stations in Beijing, Tianjin, and Hebei provinces and consider the hazard, exposure, and vulnerability factors. The results showed that for the two time periods considered, the areas with the lowest (Level-1) waterlogging risk have decreased by nearly 50%, and the second-lowest (Level-2) ones have increased by nearly 55%. Although the areas at Level-3 and above have decreased by 17%, the variations in each city were quite different. Among them, the areas at Level-3 have increased by 52% and 51% in Beijing and Handan, respectively. During the years 1991–2019, the areas at Level-3 risk and above were mainly found in Beijing, Tianjin, Shijiazhuang, Qinhuangdao, Handan, and Xingtai. Among them, Beijing had the highest waterlogging risk index. In particular, the areas with Level-3 risk and above have increased by 76% in the past 30 years. The areas with the highest risk level (Level-4) of waterlogging in Beijing were mostly found in the downtown areas (Haidian, Chaoyang, Dongcheng, and Xicheng districts). This study provides a scientific background for urban waterlogging risk management and implementation of the national strategy for the development of the BTH region.