As ecosystems provide multiple supports for human life, maintaining ecosystem health is imperative to achieving sustainable socio-economic development. Although the current ecosystem health assessment method has undergone many improvements and revisions, it still needs to be improved in terms of scientificity. At the same time, it is not clear what the appropriate scale for assessing ecosystem health is. To some extent, these issues have led to barriers between theoretical research and practical planning applications of ecosystem health. In order to explore the above questions, this paper further revised the ecosystem health assessment method. The proven and reasonable vitality-organization-resilient-service model was revised by considering the neighborhood variability and anthropogenic disturbance as factors affecting the evaluation. In order to explore the differences in ecosystem health assessment results at different scales, this paper set up 8 assessment scale units from 5 km to prefecture-level city to quantitatively assess the coastal region of the East China Sea (including Shanghai, Jiaxing, Ningbo, Wenzhou, Taizhou, Ningde, Fuzhou, Putian, Quanzhou, Xiamen and Zhangzhou) ecosystem health status from 1990 to 2015. The time-series variation characteristics and spatial divergence patterns of ecosystem health in the study area were analyzed, and the scale-dependent effects of ecosystem health were also explored. The following conclusions were obtained:(1) the level of ecosystem health in the study area declined and then increased at the node of 2000 over the study time but showed an overall decreasing trend. The distribution of ecosystem health values has become more discrete since 2000, meaning that healthy ecosystems have become healthier and poor ecosystems have deteriorated. (2) Ecosystem health was highly heterogeneous in spatial distribution. Ecosystem health values were relatively low in the coastal areas, north of Ningbo, and relatively high in the hilly mountainous areas, away from the ocean. The ecological health of Shanghai city center was the poorest at small scale, and Jiaxing was the poorest at prefecture-level city scale. (3) Ecosystem health assessment work is somewhat spatial scale-dependent. The larger the study scale, the more the distribution of ecosystem health tends to average out, and the easier it is to obtain a spatial pattern distribution of change trends. The results of small-scale assessments can better explain details such as the distribution of high and low clusters of ecosystem health. As a result, there is no optimal scale of study for the assessment of ecosystem health. A multiscale set-up helps to assess ecosystem health in a comprehensive and detailed way.