Abstract: After a region was assigned specific carbon emission reduction goal, the carbon emission allowance allocation among enterprises becomes the key to the implementation of regional carbon emission reduction targets. Following fair, effective and enforceable principles, this paper proposes a new carbon emission allowance allocation model for enterprises based on information entropy and Boltzmann entropy, considering the heterogeneity of the industry and minimizing the carbon emission transaction costs in every industry. At last this paper uses the 2012 and 2013 data of above-scale industries in Kunshan to allocate the carbon emissions among enterprises in 2015. The results shows that, the carbon emissions allocation among industries based on the information entropy, considering various factors, is basically in line with industry emission reduction responsibility, ability, potential and efficiency; and the carbon emissions allocation among enterprises based on Boltzmann entropy, considering historical responsibility and future development needs, rewards the enterprise with high emission efficiency and punishes the enterprises with low efficiency, which contributes to regional low-carbon development.