Urban lakes serve multiple functions, including flood storage, water supply, landscape tourism, and ecological maintenance, thereby holding significant ecological, environmental, and socioeconomic value. The Yangtze River Basin contains approximately 355000 urban lakes, accounting for over 65% of the total water area of China's urban lakes, and these lakes exhibit strong ecological functions. However, urban lakes in the basin currently face prominent challenges such as high non-point source pollution loads during flood seasons, pollution risks associated with ecological water supplementation safety, and limited resilience of aquatic ecosystems. Addressing these issues requires an integrated approach that considers the holistic nature of urban lake ecosystems and the systemic characteristics of river basin management. It is essential to advance coordinated water environment and aquatic ecosystem management under a source-sewer-treatment plant-river-lake integrated framework. This study systematically reviews the research status and development needs related to the coordinated governance of water environment and aquatic ecosystems in urban lakes of the Yangtze River Basin. It synthesizes recent progress in domestic and international research as well as practical engineering applications, and provides an in-depth analysis of the major challenges currently constraining coordinated governance: (1) In certain urban areas, the accumulation of pollutants during dry seasons and the episodic release of contaminants during rainfall events remain prominent, the storm-induced non-point source pollution increasingly becoming a key constraint on the sustained improvement of urban water environments; (2) A critical challenge in using effluents from municipal wastewater treatment plants as ecological replenishment for urban lakes lies in achieving water quality and aquatic ecosystem compatibility between reclaimed water and receiving water bodies; (3) The ecological resilience of lake ecosystems remains weak, and watershed-level systematic governance is still insufficient. Based on this analysis, we summarize targeted strategies and key tasks centered on the framework of "efficient external source control-water supplementation safety-habitat restoration and reconstruction-system optimization and configuration-integrated platform management", aiming to accelerate progress in ecological environment governance of urban lakes in the Yangtze River Basin and provide scientific and technological support for national ecological civilization construction and the implementation of green development strategies.