[Objective] Under total carbon emission control, a fair and scientific allocation of carbon emission quota among provinces is a key approach to achieve the goal of "double carbon", as well as an important cornerstone of the carbon emission trading system. The marginal cost of carbon emission reduction in the results of carbon emission quota allocation under different scenarios was analyzed, with a view to determining the optimal carbon emission quota allocation scheme at the lowest cost, providing a theoretical basis for the subsequent regional allocation work and a reference for the formulation of regional carbon emission reduction schemes. [Methods] The ecological index was introduced on the basis of the carbon quota allocation index established by predecessors, and four scenarios including equity, efficiency, ecology and equity-eco-efficiency were set. The SBM dual model was used to calculate the regional marginal carbon emission reduction cost under different scenarios, and the optimal allocation scheme was determined based on this. [Results]The results show that: Under the scenarios of fairness, efficiency, ecology and consideration, the average marginal cost of carbon emission reduction was 0.295 million yuan/t, 0.312 million yuan/t, 0.291 million yuan/t, and 0.309 million yuan/t, respectively. The emission reduction cost of the scheme introducing ecological index is significantly lower, and it can be inferred that the carbon sink offsets part of the carbon emissions which are difficult and costly to reduce emissions. The cost of emission reduction under the balanced scenario is significantly higher than that under the fair and ecological scenarios, indicating that the improvement of carbon emission efficiency will lead to the increase of marginal carbon emission reduction cost. [Conclusion] The carbon emission quota under ecological scenario is the best scheme to achieve the "double carbon" goal with the lowest marginal carbon emission reduction cost, and can be used as a reference for the formulation of regional carbon emission plans.