The scientific and reasonable allocation of initial carbon emission rights is the foundation of establishing and perfecting the carbon trading system, which is directly associated with the completion of carbon emission reduction targets. Guided by the rational distribution of China's carbon emission rights, this paper adopts a multi-index method to investigate the initial distribution of China's carbon emission rights from a regional perspective according to the comprehensive principles of fairness, efficiency, sustainability, and environmental capacity limit. The results show that the use of regional historical carbon emissions or economic factors as a single indicator of carbon emission rights distribution is unreasonable according to historical emissions or GDP, and the results are quite different from the actual demand. Under the overall coordination degree allocation model, it is reasonable for Region 2, Region 3, and Region 4 to undertake higher emission reduction responsibilities, and the emission reduction tasks in these regions are likely to be completed, which shows that the carbon emission rights allocation under the comprehensive principle is more in line with the actual demand and has good operability, robustness, and compatibility. The allocation of carbon emission quota requires the scientific and reasonable formulation of the total national allocation, that all provinces and cities can form a stable quota expectation, effectively design the allocation principle scheme, give consideration to fairness and operability, and do not share the responsibility of regional emission reduction with a one-size-fits-all approach.