The risk of urban waterlogging is increasing with global climate change and rapid urbanization, especially for urban agglomeration like Beijing-Tianjin-Hebei (BTH) region. In this study, we obtain the urban waterlogging risk index of the BTH urban agglomeration and considering the hazard, exposure, and vulnerability factors, we assess waterlogging risks in the built-up area of the BTH for two 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. The results showed that for the two considered periods, the area with the lowest (level 1) waterlogging risk has decreased by nearly 50%, and the second-lowest (level 2) ones have increased by nearly 55%. Although the area higher risk has decreased by 17%, the difference among each city is quite large. 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 with risks of level 3 and above are mainly found in Beijing, Tianjin, Shijiazhuang, Qinhuangdao, Handan, and Xingtai. Among them, Beijing has the highest waterlogging risk. In particular, the areas with risk of level 3 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 and regional strategy for the development of the BTH region.