At present, environment is deteriorating at a rapid pace. Traditional economic system and the environmental system is division. It is harmful to the current environmental protection work. Exploitation of Environmental Economic Decision Support information System (EEDSS) is based on the current environment and economic situation requires, and becomes a keystone. Taking environment economy system as a research object according to system engineering methodology and large-scale system theory, and integrating the computer GIS technology, environmental science, economy, this paper analyzes the structure and mechanism of environment economy system (EES),the logic structure, system structure and function structure were brought out, provides a EEDSS model. EEDSS focus on projection of economic environmental information management and decision-making support. In EEDSS, the information data of society economy and environment are saved, managed, shared and analyzed by the technique of GIS. It provides a scientific management and decision support for the development of environment economy.