Model system is the most important part of the DSS. The key point of Decision Support System for Economic Development and Environmental Protection is that the change of the environment is caused by the economic development. Analyses show that different policy systems bring different economic state, and different economic states result in different environmental state characters. Firstly, according to the principle, the model system shows the policy classification including object layer, decision layer and state layer. Secondly, the logic model between economic development and environmental protection is introduced. For the more, the main models are put forward on three levels including assessment model, analysis model and decision model. At the end of the paper, the structure of the DSS and the running process of the model are displayed.