In this research, Iran’s energy system is simulated with the aim of reducing the greenhouse gases (GHG) emissions. Key variables of the system are identified according to expert’s viewpoints, and their relationships are depicted through a “cause and effect” diagram. Then, the mathematical equations which denoting variables’ relations are written according to the literature as well as some methods such as regression. Eventually, different scenarios for allocation of energy resources to end-users, including residential and commercial, agriculture, transportation, industries and power plants are simulated and the one that resulted to reduce the GHG emission in long-term is selected for implementation. Designing a dynamic model of the energy system and its simulation helps decision-makers to investigate other managerial policies as well as their effects on increasing the productivity of the system in the future.