<p>In many lake basins, connections between lakes and rivers have been severed to mitigate flood risks and develop the social economy. This isolation may degrade the ecological quality of lake basins, yet comparative studies on the ecological qualities of connected and disconnected lake basins are scarce. In this study, we evaluated the spatiotemporal variations in the ecological quality and driving factors between connected (Shijiu Lake) and disconnected (Shengjin Lake and Longgan Lake) lake basins in the lower reaches of the Yangtze River from 2000 to 2023 using the Google Earth Engine platform, with water bodies masked via the Modified Normalized Difference Water Index. The results revealed that the remote sensing ecological index (RSEI) of the three basins generally increased but with distinct changing trends. The river-connected Shijiu Lake Basin presented a higher RSEI than the disconnected Shengjin and Longgan Lake Basins from 2005–2010, while the opposite was observed from 2015–2023. RSEI hotspots were primarily distributed in mountainous areas, while cold spots were mainly around lake areas. The main drivers of RSEI in the Shijiu Lake Basin were land use intensity and its interactions, whereas in the Shengjin Lake Basin, changes were primarily driven by forest cover change and its interactions. Our results emphasized the role of anthropogenic activities such as land use and forestation in driving the changes of RSEI in the lake basins of the Yangtze River. The low ecological quality in connected lake basins during 2015–2023 and the dense cold spots of RSEI around lake areas suggest that current ecological restoration projects should be prioritized in connected lake basins of the Yangtze River, especially around lake areas.</p>