Ecological security is gaining importance for its role in human development, as traditional risk factors are being increasingly replaced by threats such as ecological and environmental changes. Taking the example of Xiamen estuary, a typical estuary in southern China, our research focused on the problems related to ecological security, caused by the degradation of ecosystem service and function. We propose an evaluation index system for assessing the ecological services, and standardize ways to determine the evaluation standards and weights. The results show that the ecological security index for Xiamen estuary is 57.1, indicating a “warning” state. This implies that the ecosystem there has been damaged to some degree, and its systematic structure is deteriorating. Twelve indices showed a score below 60, four of which belong to the category of supply services. The study shows that there are some problems associated with the ecological services in Xiamen estuary. The indices that were considered as unsecure include fish density, marine trophic level, primary productivity of water bodies, alien species invasion risk, and species diversity. We conclude that these problems are mainly caused by human activities such as over-fishing, reclamations, and industrial and agricultural pollution. Display omitted