The European Commission has proposed the “Fit for 55” draft to address the emission reduction goal of the shipping industry within the European Union (EU) through the market mechanism measures. In order to evaluate the taxes and fees that ships will need to pay in the EU region in the future, the components and influencing factors of the EU taxes and fees are discussed to propose three measures to reduce the EU taxes and fees. These three measures are compared and analyzed for the large container ships. The study shows that using low and zero carbon fuels is the trend for reducing carbon emissions in the future.