Evaluation study on the estuarine ecosystem is the foundation and basis for ecological studies in the estuary area. In this paper an index system for estuarine eco-health evaluation of Zhangweixin River is established, with 15 indexes in three major types of indicators: such as environmental, ecological and socio-economic, by using the analytic hierarchy process (AHP). Multi-criterion analysis is used to evaluate the estuarine eco-health of Zhanweixin River. The results indicated that the period of river flow cut-off and phytoplankton diversity were important indexes for evaluating estuarine eco-health of Zhangweixin River. The main cause of the unhealthy status of the estuarine ecosystem of Zhangweixin River is related to the significant reduction of water flowing into the sea. As the basis of study on estuarine eco-environmental water demand, evaluation results provide basic support for the research on improving the estuarine ecoenvironment by utilizing flood resources.