In response to the prominent issues of coordinated governance of urban waterlogging and rainy season pollution in the middle and lower reaches of the Yangtze River, this paper discusses three aspects including urban water safety, risk of black and odorous return of rainy season water bodies, and ecological degradation of river and lake water. It is found that the urban river network in the middle and lower reaches of the Yangtze River is characterized by high density, heavy precipitation, frequent rainstorm, dense population, high level of economic development, and prominent water problems such as waterlogging, pollution and ecological degradation.Frequent urban waterlogging and pollution during the rainy season have caused some urban water bodies to return to black and smell, seriously affecting the quality of urban water environment and becoming an important bottleneck problem that restricts the green development of cities in the middle and lower reaches of the Yangtze River. Suggestions were put forward to establish a three-level collaborative governance system for waterlogging, construct a coupling engineering system for urban “green-gray-blue” facilities, and coordinate the improvement of water quality and ecological restoration. Keywords: Cities in middle and lower reaches of the Yangtze River; urban waterlogging; rainy season pollution; collaborative governance; green development