Ecological vulnerability is an important constraint to sustainable, high-quality economic development. In this paper, 38 districts and counties in Chongqing Municipality are the object of study, and 12 representative indexes are selected using the SRP (Sensitivity-Recovery-Pressure) conceptual model. Principal component analysis (PCA) and geographic information system (GIS) are used to evaluate and analyze the ecological vulnerability of Chongqing, and the driving factors are identified by Geodetector. Finally, the ecological vulnerability of Chongqing in 2025 is predicted by the gray prediction model GM(1,1). The results show that: 1) The ecological vulnerability of Chongqing Municipality from east to west is characterized by a “low-middle-high” distribution with obvious regional heterogeneity. 2) From 2010 to 2020, there is a trend of “overall stabilization but local enhancement”. The migration from moderately and above vulnerable areas to more highly vulnerable areas is significantly higher than the migration to micro and mild vulnerability areas, which is due to socio-economic and vegetation factors dominating the region. 3) In 2025, moderate vulnerability will expand spatially in the northeast of Chongqing Municipality, while severe and extreme vulnerability will move to the periphery and the east. The results of this study can provide a theoretical basis and decision support for ecological environment protection and sustainable development of Chongqing.