Carbon emission permit trading is widely considered an effective means to achieve optimal distribution of regional environment. The initial allocation of carbon emissions is the bases of the successful implementation of industry carbon trading. Developing low carbon economy and achieving the state’s energy saving targets are effective ways to the adjustment of economic structure, the improvement of energy efficiency and the development of new industries. The initial allocation of carbon emissions trading has a significant impact on the carbon emissions trading policy. The paper provides a theoretical basis for the choice of the allocation methods of carbon emission permit trading through the research on the fairness of carbon emission trading.