Abstract: Taking the five lake basins of the central Yunnan Plateau as the study areas, based on the eco-environmental evaluation system of “function-stability-stress", the ecological quality index (EQI) was constructed to characterize the eco-environment. Comprehensively adopting the Theil-Sen slope estimator, Mann-Kendall test, random forest model, the eco-environmental changes and driving factors in the lake basin of the central Yunnan Plateau over a long period from 2001 to 2021 were analyzed. The results showed that: (1) The eco-environmental quality of the lake basins in the central Yunnan Plateau showed a slow fluctuating downward trend from 2001 to 2011, with EQI decreasing from 0.569 to 0.549. After 2011, the improvement was more significant, and by 2021, EOI had reached its highest point of 0.577, showing an overall upward trend. This was related to the region's vigorous implementation of returning farmland to forests and grasslands, afforestation, ecological relocation, and restoration since 2007. (2) Among the five major lakes, the eco-environmental quality of Yangzonghai and Fuxian Lake basins showed a significant upward trend from 2001 to 2021. Among them, the EQI of Yangzonghai basin increased from 0.615 to 0.668, and the EQI of Fuxian Lake basin increased from 0.621 to 0.671. Dianchi Lake Basin maintained a relatively stable state from 2001 to 2021, with an EQI of 0.562 in both 2001 and 2021. The eco-environmental quality of Xingyun Lake and Qilu Lake basins significantly declined from 2001 to 2021. The EQI of Xingyun Lake basin had decreased from 0.553 to 0.549, and the EQI of Qilu Lake basin had decreased from 0.534 to 0.518. The areas with good and significantly improved eco-environmental quality in the five major lake basins were mainly distributed near the boundaries of high-altitude basins, while the areas with poor and significantly decreased quality were mainly distributed in the lower altitude lake basin areas. (3) The factor importance results showed that the ecological function index was the most important for basin ecology, followed by population density, which was as the second dominant factor, and due to the unique topographical conditions and GDP distribution, the smallest impact was the slope and the gross domestic product on the basin's eco-environment. Converting farmland to forests and grasslands significantly improved the eco-environment, while construction land rapidly encroached on forests and grassland, causing a significant decline in the eco-environment. The research results can serve as a reference basis for the development, management, and ecological protection and governance of lake basins in the central Yunnan Plateau.