As the issues of renewable energy utilization and environmental pollution become increasingly prominent, to further improve renewable energy efficiency and achieve low carbon emissions, it is necessary to configure the Integrated Energy Production Unit (IEPU) capacity and establish a low-carbon economic operation strategy for the IEPU. By selecting the Chinese certified emission reduction (CCER) quota mechanism, the comparison of configuration results under the traditional carbon trading model without CCER quotas and the ladder-type carbon trading model with CCER quotas, analyzing the synergistic effects between the reward and punishment ladder-type carbon trading mechanism, carbon trading quotas, and capacity configuration, taking into account the impact of the types of device configuration on carbon emissions. To constrain carbon emissions, the reward and punishment ladder-type carbon trading mechanism is introduced, as well as the CCER quota, this paper establishes an optimal full life-cycle cost model, achieving a reasonable capacity configuration for devices with low-carbon effects in the system. Finally, through the analysis of various scenarios, the effectiveness of the proposed capacity configuration strategy is compared and verified, and the most sensitive interval segment of the ladder-type carbon trading parameters is analyzed. Ultimately, renewable energy consumption is improved, and the environmental and economic benefits of the IEPU system are realized.