To achieve the carbon reduction target, the Chinese government not only requires a quota allocation scheme in line with the current development situation, but also needs to minimize the economic expenditure in the emission reduction work. Therefore, this study integrates the multi-index method and zero-sum gains–data envelopment analysis model to obtain a fair and efficient multi-criteria quota allocation scheme. To ensure the effectiveness of the scheme, the fairness and cost effect of the scheme are quantitatively tested. In addition, regional cooperation factors are introduced into the research framework to providing feasible practical measures. The results show that: (1) After optimization, the eastern region has the largest quota increment, accounting for 45% of the country’s quota. (2) The multi-criteria quota allocation scheme after secondary allocation is a more ideal scheme. The quota scheme not only meets the requirements of fairness and efficiency, but also has lower abatement costs. (3) Regional cooperation should be encouraged by China, especially the eastern region, which can alleviate the reducing emission pressure through cooperation. Although the western region needs to undertake additional emission reduction tasks, it can improve the utilization rate of local renewable resources and be conducive to long-term economic development. These results will provide a reference for China to achieve its carbon reduction targets.