Abstract: At present, the treatment of urban black and odorous water bodies in China has achieved good results, but the post-rain recurrence in the rainy season has become a new environmental problem faced by urban areas, and there is a lack of research on the risk of black and odorous water bodies in the rainy season. This study took 88 cities in the Yangtze River Basin as the research object and analyzed the daily precipitation of each city from 2019 to 2023. Based on the number of days of over-threshold rainfall, the risk of black and odorous urban water bodies in the Yangtze River Basin was evaluated by the Z-value method, and the mechanisms behind the post-rain recurrence were discussed. The results showed that: (1) Rainfall as the main driving force caused the overflow of the combined pipe network, and the surface runoff caused by rainfall carried high-concentration pollutants into the water bodies, which were the primary causes of post-rain black and odorous conditions. (2) From 2019 to 2023, the total frequency of daily precipitation ≥10 mm in 88 cities in the Yangtze River Basin ranged from 33 to 128 events. When the 24-hour precipitation ≥10 mm and reached moderate rain or above, the overflow was very likely to occur. (3) On the spatial scale, the risk of post-rain black and odorous conditions in cities in the Yangtze River Basin showed a trend of increasing from the upstream to the middle and lower reaches. 15%-41% of the upstream cities were in the low risk range (Z<−1); 67%-80% of the cities in the middle reaches were in the medium risk range (−1≤Z≤1), and 20%-30% were in the high risk range (Z>1); 48%-84% of the downstream cities were in the medium risk range, and 12%-40% were in the high risk range. The cities in the Yangtze River Basin shifted among three risk levels. The upstream cities mainly shifted between low risk and medium risk, while the middle and downstream cities mainly shifted between medium risk and high risk. (4) The impact of rainfall on urban water bodies was manifested in two aspects: the input of large pollutant loads by multiple rainfalls and the input of high-concentration pollutants by a single rainfall. Cities with large pollution loads were often at medium or high risk, and the rainfall reaching overflow standard event could often discharge mild or severe black and odorous water into surface water bodies, thereby causing black and odorous conditions.