With rapid economic development, energy consumption and environmental pollution have become increasingly prominent, making clear emission reduction targets necessary. Therefore, this paper forecasts input and output variables for China’s six industries during the 13^th Five-Year Plan by using an EBMDEA model to analyze the distribution efficiency of the industries. Moreover, the ZSG-DEA model is used to optimize carbon emission quotas and establish a reasonable distribution plan. The results show that among the six major sectors in China, the initial allocation of carbon emission rights has relatively low DEA efficiency, with significant efficiency differences among sectors. Only agriculture, forestry, animal husbandry, and fisheries achieved an efficient initial allocation of carbon emission rights, whereas industry and transportation, warehousing, and the postal service exhibited low allocative efficiency. The industrial sector has the greatest room for adjustment and its reduction can be compensated for through an increase in emissions from the other sectors so as to keep total carbon emissions constant. Based on the conclusions of the study, we make suggestions for various stakeholders.