With the increasingly strict environmental regulations, the relationship between supply and demand of ships in the post-epidemic era is tense, and ship operators are under tremendous pressure. In view of the existing strict sulfur emission reduction regulations and ship freight operating at high levels in the post-epidemic era, ship operators must choose cost-effective compliance options to create better environmental benefits. This study uses a cost-effective framework to analyze ship operations Supplier’s fuel switch and marine natural gasoline compliance options, and apply these options to specific liner routes through China’s SECA. We selected an international freight liner as the research object, and calculated the net present value of the compliance option in consideration of the fuel cost of the ship, the installation and operation and maintenance costs of the compliance option. The study mainly considered the influence of the navigation distance in the emission control area on the proportion of the total navigation distance, and also considered the fuel price difference that has a greater impact on ship operating costs. Our results show that in the post-epidemic era, in accordance with the requirements of environmental protection regulations, considering the ratio of SECA and the price difference between MGO and high-sulfur fuels, the use of fuel conversion is a necessary option. We also calculated the emissions of ships, and the results show that with the expansion of the emission control area, the use of MGO can achieve better emission reduction effects. Our results show that in the post-epidemic era, Considering the ratio of SECA and the price difference between low-sulfur and high-sulfur fuels, fuel conversion is the best option. We also calculated the emissions of ships, and the results show that with the expansion of the emission control area, the use of MGO oil can achieve better emission reduction effects.