Climate change, eutrophication, and habitat fragmentation are ubiquitous ecological problems in the world. It is important to conduct scientific assessment of the external pressure and the resilience of ecosystems for the ecological management and restoration. In the case of the Yangtze River Estuary, as the end of the basin, huge amounts of pollutants were carried into the area, which resulted in the degeneration of the ecosystem during the past decades. However, little is known about the tendency of ecological vulnerability in this area under the effects of human activities and climate change. Consequently, the ecological vulnerability in the Yangtze River Estuary was assessed using geographic information system (GIS) software combined with spatial principal component analysis (SPCA). An analytical hierarchy process (AHP) was used to determine the evaluation factor weightings. According to the ecological vulnerability index (EVI) values, the eco-environmental vulnerabilities of the study area were classified into five levels:potential (< 0.5), light (0.5-0.8), moderate (0.8-1.0), heavy (1.0-1.2) and very heavy (1.2-1.5). The results showed that the inner mouth area of the Yangtze River Estuary was the most vulnerable. There was a significant decrease tendency in EVI from the inside to the outside of the mouth. The spatial distribution of the very heavy vulnerable areas within the mouth has shifted southward in the last five years. The extremely vulnerable area of about 2000 km² has changed in the assessment area with extremely vulnerable area decreased by 7% and severely vulnerable area decreased by 5%. One the other hand, the ecological environment status out of the Yangtze River Estuary has obviously improved from 2013-2017. In general, the input of large amount of land-based pollutants and the instability of the ecosystem caused by human activity were the main factors for the high vulnerability of the Yangtze River Estuary.