The Five Lakes Basin of Central Yunnan Plateau (FLBOCYP) is located in the core area of Yunnan Province and has a developed economy, but the ecological and environmental problems in the basin are serious and the sustainable economic development is threatened. The analysis of ecological carrying capacity change and the study of influencing factors in the basin is conducive to protecting the ecology of the basin and maintaining the sustainable development of the social economy. Ecological carrying capacity is an important indicator for the quantitative assessment of regional sustainable development, and the assessment of regional ecological carrying capacity based on grid scale can more accurately and vividly reflect the regional sustainable status and provide reference for regional coordinated development. With the support of GIS technology, based on the unique ecosystem characteristics of the river basin itself, the research method of quantifying the ecological carrying capacity from the three perspectives of ecological function elasticity, resource and environmental capacity and socio-economic coordination was carried out, and a relatively complete comprehensive evaluation index system of ecological carrying capacity was constructed. The ecological carrying capacity of the five major lake basins of Qilu Lake and Yangzonghai from 2000 to 2018 was evaluated, and the temporal and spatial changes and driving mechanisms of ecological carrying capacity were analyzed. The results show that: (1) The FLBOCYP has an overall moderate ecological carrying capacity (average of ~0.5). The temporal trend in ecological carrying capacity was an initial rise followed by a fall, but there was an overall increasing trend at a rate of 0.019. (2) Areas with a strong ecological carrying capacity were mainly distributed in the mountainous and semi-mountainous regions outside of the lake area, whereas areas of weaker ecological carrying capacity were mainly distributed in the plain area around the lake. The ecological carrying capacity gradually increased from the area around the lake to the periphery. (3) At a basin scale, the ecological carrying capacities of the Dian, Fuxian, and Yangzong lake basins were relatively high, whereas those of the Xingyun and Qilu lake basins were relatively low. The greatest increase in ecological carrying capacity of Fuxian Lake has occurred since 2000. (4) The spatial pattern of ecological carrying capacity showed clear agglomeration. This agglomeration has been continuously enhanced but remained relatively stable over the past 19 years. The main agglomeration modes were identified as “high-high” (HH), “low-low” (LL), and “not obvious agglomeration”. (5) Among the many driving factors, ecological elasticity, biological abundance index, proportion of forest land, and degree of human disturbance showed the greatest explanatory power for spatial differentiation of ecological carrying capacity, and the interaction of any two factors affected the spatial analysis of ecological carrying capacity even more. In summary, the overall ecological environment of the FLBOCYP has experienced significant improvement since 2000, whereas that of the plain area has deteriorated more seriously in recent years.