Economic development, accompanying with environmental damage and energy depletion, becomes essential nowadays. There is a complicated and comprehensive interaction between economics, environment and energy. Understanding the operating mechanism of Energy-Environment-Economy model (3E) and its key factors is the inherent part in dealing with the issue. In this paper, we combine System Dynamics model and Geographic Information System to analyze the energy-environment-economy (3E) system both temporally and spatially, which explicitly explore the interaction of economics, energy, and environment and effects of the key influencing factors. Beijing is selected as a case study to verify our SD-GIS model. Alternative scenarios, e.g., current, technology, energy and environment scenarios are explored and compared. Simulation results shows that, current scenario is not sustainable; technology scenario is applicable to economic growth; environment scenario maintains a balanced path of development for long term stability. Policy-making insights are given based on our results and analysis.