China’s carbon peaking and carbon neutrality targets have created huge challenges for all the economic sectors in China, including the shipping industry. Various emission reduction measures, such as Waste Heat Recovery Systems (WHRSs), Drag Reduction Coatings (DRCs), and Slow Steaming (SS), are the main options for container ship companies to select in advance. This paper aims to find the optimal combination of measures for container ship companies to reach the carbon reduction targets, which are mainly set according to the carbon reduction requirements of the International Maritime Organization (IMO). A 0–1 integer programming model is proposed under the Maritime Emissions Trading Scheme (METS) to help container ship companies select the optimal combination of measures in the context of carbon peaking and carbon neutrality. Our results show that combination 6 (using a WHRS alone and a 5.0% reduction in the original speed) is the most suitable solution with the selected values of parameters. Sensitivity analyses of the parameters are performed, such as bunker price, the auction and purchase prices of carbon and incentive levels. From the sensitivity analysis, it is found that using a WHRS is the optimal combination of abatement measures within the fluctuation range of the parameters. At the same time, according to the results, container ship companies could choose the most appropriate and profitable strategy in the dual-carbon context. Therefore, container ship companies and policymakers have access to relevant carbon reduction suggestions to encourage the implementation of carbon reduction initiatives.