After30years of reform and opening up, economic development level and the level of industrialization gap between districts and counties of Chongqing and gradually expand. The gap between the county economic development level and the level of industrialization, resulting in the total amount of major pollutants around index distribution is extremely uneven. Zoning Adjustment in accordance with the general requirements of the state of development of Chongqing and urban and rural development, the main function of the strategic plan, the suburban districts and counties to speed up the development of industry chain from the main city to the outer suburbs transfer is imperative. The low level of industrial development to meet the late start of the county industrial economy rapid development of the rigid requirements of the aggregate indicators in order to ensure the successful implementation of the industrial chain transfer and the main functional areas to adjust the Chongqing municipal government decided to start in2012the main city to carry out the work of sulfur dioxide emissions trading. Sulfur dioxide emissions trading work to be carried out, it will inevitably have to relate to the pricing of the sulfur dioxide emission rights, it is one of the basic conditions of effective emissions trading. Sulfur dioxide emissions trading pricing of the main city of Chongqing, is the effective guarantee of the main city of the sulfur dioxide emissions trading.In the background and basis of the initial distribution and price of the main city of Chongqing sulfur dioxide emission rights. In this paper, the theoretical results and practical experience to learn from domestic and international emission rights initial allocation and pricing methods, the initial allocation of emission rights theory and natural resource pricing methods, focusing on the initial allocation of emission rights and emission rights pricing methods for system analysis, combined with the initial allocation of emission rights work practice at home and abroad and the actual situation of the sulfur dioxide emissions of the main city of Chongqing, trying to build the main city of Chongqing sulfur dioxide emissions trading pricing model to determine the sulfur dioxide emission rights from the beginning of the main city the beginning of allocation and distribution prices, the policy basis and technical support for the main city of Chongqing sulfur dioxide emissions trading is going on smoothly.The main research contents include two aspects, the initial allocation of the main city of the sulfur dioxide emission rights is the choice of what kind of distribution, and the second is to determine the allocation and how to determine the initial distribution price. The specific contents are as follows:(1) the choice of the initial allocationFor now, many provinces in China have chosen in the initial allocation of emission rights issue are distributed free of charge, but the free allocation of emission rights is contrary to the basic principles of the market economy, cannot guarantee the fairness of the distribution, so that enterprises lack of emission reduction amount of power and pressure, it is difficult to achieve the effect of pollution control. The final trend of the initial allocation of emission rights should be paid configuration.(2) determine the price of the initial allocationPaid the initial allotment, it is inevitable to determine a reasonable initial allocation price or emissions trading work will not be able to long-term effective pursued. Select a proper and effective pricing method to determine the price of the initial allocation of emission rights is studied in this paper.Articles through a comparative analysis found that the initial allocation of paid allocation is better than free allocation, the main city of Chongqing initial sulfur dioxide emission rights allocated to the sale of government pricing is more suitable for the actual situation of Chongqing; pricing method, the choice of re-replacement cost method to calculate the initial allocation more reasonable prices, better operational operation.