Based on the "pressure-state-response (PSR)" concept model, a degradation evaluation index system was constructed for the cropland, wetland, and inshore ecosystems in Dongtan coastal zone of Chongming. By using multiplication synthesis, a combination of analytic hierarchy process and entropy weight method, the weights of each evaluation index were obtained, and, through geographical space index quantification and spatial clustering, the degradation degree of each ecological system was analyzed. The results showed that the degradation degree of Dongtan coastal ecosystems in 2005 could be spatially classified into four classes, i.e., class I, class II, class III and class IV, with the degradation degree aggravated increasingly. For the cropland, wetland, and inshore ecosystems, the weight of heavy metals was the largest, being 0.65, 0.20, and 0.26, respectively. Bird diversity index, land use degree, and Spartina alterniflora coverage also had greater effects on wetland ecosystem, and their weights were 0.26, 0.16, and 0.10, respectively. For cropland ecosystem, land use degree was also an important affecting factor, with the weight of 0.22.