Global change and human disturbance have significantly influenced the eco-environments on which humankind depends, and have increased the ecological vulnerability of these environments. The vulnerability of the eco-environment in the Three Gorges Reservoir Region has been a great concern in recent years. This region plays an important role in the ecological function of the upper reaches of the Yangtze River, China; yet, it is subject to intensive human disturbance, making it particularly vulnerable, especially the areas in Chongqing Municipality where the economy is in a rapid development. Spatially explicit ecological vulnerability assessment has been regarded as one of the significant tools for ecological restoration and protection for many years. This study quantitatively evaluated ecological vulnerability in the Three Gorges Reservoir Region in Chongqing Municipality from 2001 to 2010 through the use of remote sensing (RS) and geographical information system (GIS) techniques. The ecological vulnerability distribution and its dynamics over the decade were analyzed, in addition to the factors that drive ecological vulnerability dynamics, after the establishment of an evaluation system. The evaluation system contained 18 indicators (including natural and anthropogenic factors), based on the Pressure-State-Response (PSR) frame model, which emphasizes both the natural quality of ecosystem health and the integration between these natural qualities and human attributes. Using spatial principal component analysis (SPCA), the ecological vulnerability index (EVI) in different years in the study region was then calculated, followed by standardization. The standardized EVI value was classified into five levels (negligible, light, medium, strong, and extreme), based on equal interval classification. Using the different ecological vulnerability levels over the study decade, the ecological vulnerability synthetic index (EVSI) in the area was calculated. The results showed that from 2001 to 2010, the ecological vulnerability in the study area was at a medium level, and that it showed a noticeable spatial distribution pattern. The strongly and extremely vulnerable areas were mainly distributed in the central and western parts of the study region, while the negligible and lightly vulnerable areas were located in the northeastern and southeastern parts of the study region. The EVSI value changed significantly inter-annually, with a minimum of 2.37 in 2002 and a maximum of 2.99 in 2008. The EVSI value continuously increased after the impoundment of the Three Gorges Reservoir in 2003, and decreased after 2008. In addition, ecological vulnerability in the study region was caused by interactions between natural and anthropogenic factors, in which urban residential pollution, soil erosion, and vegetation condition were the most important factors. There was also a spatial trend of polarization in the ecological vulnerability. In the seriously fragile regions, eco-environmental conditions declined whereas eco-environmental conditions gradually improved in mildly fragile regions.