Low carbon development for supply chain is an important way to seek the development mode of low carbon economy. In this context, firms should optimize low carbon behavior of every node firm and the whole supply chain from the view of supply chain, to solve carbon emission problem through cooperation of firms in the supply chain, and to implement low carbon supply chain management. Currently, the theoretical research and legislative practice on low carbon economy are still in their initial stages in China. Many firms did not still pay enough attention to low carbon development, who are lack of power to apply the new technology of the energy saving and emission reduction. In order to encourage enterprises to use low carbon technology and promote the energy saving and emission reduction, the government can formulate economy prompting policies. Among these policies, the marketable pollution permits is an effective economic lever, which can realize to decrease pollution emission. In this paper, the effect of the marketable pollution permits on the decision behavior of each decision-maker is analyzed in the supply chain network, and an equilibrium model is proposed in supply chain context, to study how government should allocate initially the pollution permits to obtain assigned environmental goal. Hence, a supply chain network with multi-pollutant and multi receptor points is developed. The investment in production technology and emission-abasement technology is included. The equilibrium patterns for the supply chain network with marketable pollution permits are analyzed. The variational inequality framework is given. The equilibrium model is developed. The model deals explicitly with spatial differentiation and also guarantees that the imposed environmental standards are met through the initial allocation of licenses. A solution algorithm for the model is proposed. Finally, numerical examples are solved by using the proposed model and algorithm. The profit-maximized quantities of oligopolistic firms' products and the quantities of emission, along with the equilibrium allocation of licenses and their prices, as well as the optimal investments in the technologies for the supply chain network are computed. Moreover, the effect of changes in investment cost parameters, the number of firms on the investment measures for production and emission-abatement technology are illustrated. The study can guide firms in the supply chain network to join the ranks of low carbon and implement production mode of low carbon economy, and provide decision-making basis for relevant departments of government to design the pollution permits system.