[Objective] Under total carbon emission control, an equitable and scientific allocation of carbon emission quota among provinces of China is a key approach for achieving the “dual carbon” goal, as well as an important cornerstone of the carbon emission trading system. The marginal cost of carbon emission reduction was analyzed under different scenarios with regard to the results of carbon emission quota allocation in order to determine the optimal carbon emission quota budget scheme at the lowest cost, thereby providing a theoretical basis for subsequent regional allocation work and a reference for the formulation of regional carbon emission reduction schemes. [Methods] An ecological index was introduced based on the carbon quota budget index established in previous studies. Four scenarios (including equity, efficiency, ecology, and balanced equity-efficiency-ecology) were evaluated. The slacks-based measure (SBM) dual model was used to calculate the regional marginal carbon emission reduction cost under different scenarios, and the optimal budget scheme was determined based on these results. [Results] Under the scenarios of equity, efficiency, ecology and balanced, the average marginal costs of carbon emission reduction were 0.295 million yuan/t, 0.312 million yuan/t, 0.291 million yuan/t, and 0.309 million yuan/t, respectively. When the ecological index was introduced, the emission reduction cost of the scheme was significantly lower, and it can be inferred that the carbon sink offsets a portion of the carbon emissions that are more difficult and costly to reduce. The cost of emission reduction under the balanced scenario was significantly higher than under the equity and ecology scenarios, indicating that improvement in carbon emission efficiency will lead to an increase in marginal carbon emission reduction cost. [Conclusion] The carbon emission quota under the ecology scenario was the best scheme for achieving the “dual carbon” goal with the lowest marginal carbon emission reduction cost. Attention should be paid to the formulation of regional carbon emission schemes and carbon trading mechanisms.