To carry out the diagnosis and evaluation of the ecosystem health in Yuxi three-lake watershed, this paper presents the changing trend of its health state, and predicts the future development. This also provides ideas for maintaining the regional ecosystem health, and then gradually improves the ecological environment quality. Taking Fuxian Lake, Qilu Lake and Xingyun Lake (the three-lake watershed) in Yuxi City, Yunnan Province, Southwest China as the research object, a model combining pressure-state-response and kernel density estimation (PSR-KDE) adopts to diagnose and evaluate the ecosystem health of the "three lake" watershed from 2010 to 2020, and the distribution map of ecosystem health index has obtained by the evaluation indexes integration based on GIS spatial analysis. Hence, the evaluation results have visualized on the map. The results show that: The distribution of ecosystem health index in the study area was 0.1530–0.7045 in 2010, 0.2056–0.7512 in 2015, and 0.2248–0.7662 in 2020. 0.12% was in the pathological area in 2010. After 2015, the pathological condition of ecosystem health has completely solved, and the proportion of unhealthy ecosystems was 11.95% in 2010, 7.38% in 2015, and 5.97% in 2020. The ecosystem health index of the study region was 0.5523 in 2010, 0.5807 in 2015, and 0.5815 in 2020, it indicates that the ecosystem was in a sub-health state. From 2010 to 2020, the ecosystem health around Qilu Lake was the most worrying, followed by the northwest of Fuxian Lake and the northern and southern regions of Xingyun Lake. The ecosystem health of the three-lake watershed showed significant improvement from 2010 to 2020. The study ecosystem health assessment and early warning in the three-lake watershed is significant to the ecological environment protection and management of the plateau lake basin, the restoration of the territorial space ecology and the economic development of the surrounding area. •Build the three-lake watershed ecosystem health evaluation model of PSR-KDE.•Ecosystem health of three-lake basin from 2010 to 2020 was diagnosed and evaluated.•Achieve a distributed effect on the map for ecosystem health.•In 2010, 2015 and 2020, the ecosystem of three-lake basin was in a sub-healthy state.•The government has been actively and vigorously maintaining the ecosystem health.