Abstract: As one of the largest carbon emitters in the world, China regards carbon emission trading as an important measure of national energy conservation and emission reduction strategy. Scientific and reasonable allocation of provincial carbon emission rights is the core issue of carbon emission trading. It is also essential for China to meet its emission reduction targets. This paper studies how to make initial allocation of China's total carbon emission permit from the perspective of balancing the two principles of fairness and efficiency. In the aspect of fairness principle, the historical average principle, population average principle and the principle of average ability to pay are compared and analyzed, and the average distribution principle of ability to pay is selected to be introduced into the principle of comprehensive distribution. In terms of efficiency principle, zero sum DEA model is used to determine the initial quota allocation scheme when the regional efficiency is maximized. Finally, the over-entropy method, coupling the allocation scheme of fairness principle and efficiency principle, forms the comprehensive quota allocation scheme. The research results are of great significance to the establishment of a fair and effective initial carbon quota allocation mechanism, the achivement of the national total carbon emission control target, and the promotion of China's high-quality development.