Abstract: Estuaries are transitional water zones as functional ecotones connecting rivers and oceans. Both of natural forces and human activities drive estuarine ecosystems variations. Ecological modeling plays a significant role in studying structure and function of ecosystem, simulating processes of ecosystem succession, and understanding response and feedback of biological processes on ecosystem. Hear we review different type of ecological models, and presents their features, strengths and weaknesses, as well as how apply these models to real world problems. Some critical technical questions are discussed, such as variables and functional types of model, model coupling and spatio-temporal scale, as well as parameter determination and uncertainty analysis. In particular, some instances are illustrated to demonstrate how to apply numerical models to serve estuarine integrated management schemes, including ecological engineering design, ecosystem restoration, ecosystem assessment, and system decision support. Although the ecological modeling research in China has made some processes including their applications, there is still a gap in some respects needed to be improved.