Located northeast of Yuxi City, Yunnan Province, China, the Fuxian Lake Basin is not only a famous scenic area, but also an ecological and environmental protection zone. The basin is a plateau mountainous lake region that has key ecosystem vulnerability and sensitivity. A dynamic evaluation of ecological vulnerability is important for assessing the ecological environment of a region, which is significant for the protection of ecological environments and providing ecological security early warnings. Based on remote sensing (RS) and geographic information system (GIS) technology, remote sensing data, meteorological data, and economic statistics were used to perform a vulnerability analysis for the Fuxian Lake Watershed. Using the “cause and effect” evaluation model that relies on the remote sensing image pixel as the basic evaluation unit, the ecological vulnerability and the dynamic changes of the basin were evaluated using the analytic hierarchy process (AHP) method. Data collected in 1974, 1977, 1987, 1990, 1996, 2000, 2006, 2012, and 2015 were analyzed to determine the temporal and spatial distribution characteristics and the dynamic changes over longer time-spans for ecological vulnerability. Afterward, the effects of land use and the consequential changes to ecological vulnerability were studied. The results indicated that the ecological vulnerability showed a trend of “overall stability but local strengthening” in the Fuxian Lake Basin from 1974 to 2015. The annual ecological vulnerability integrated index for the basin was 2.55±0.16, which indicates a transitional state between micro-vulnerability and mild vulnerability. On the basis of maintaining the degree of original vulnerability, the vulnerability of each grade was most commonly converted to the adjacent grade. The degree of ecological vulnerability was more commonly converted toward a more severe grade, and regions were less likely to recover from the severe vulnerability grade. The ecological vulnerability integrated index of the bare land was the highest (3.28), and the ecological environment of bare land was most vulnerable in the Fuxian Lake Basin.