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With new sulphur oxides emission limits carried out in 2020, multiple desulphurisation methods have been proposed. The main desulphurisation scrubber systems were chosen and investigated using life cycle assessment. The whole system life is divided into the construction and operational phases. Three different systems classified by desulphurisers, namely, seawater, NaOH, and Mg-based systems, were modelled in GaBi software. Moreover, environmental, economic and energy aspects (3E model) were introduced for further analysis. Through this study, some conclusions have been drawn. As for the environmental aspect, the seawater system has the most pleasing performance since the primary emissions come from 1.24E+03 kg CO2 and 1.48E+01 kg chloride. The NaOH system causes 1000 times more emissions than the seawater. The Mg-based system has less pollution than the NaOH system, with 5.86E+06kg CO2 and 3.86E+03 kg chloride. The economic aspect is divided into capital expenditure (CapEx) and operational expenditure (OpEx) to estimate disbursement. The seawater system also has the most favourable cost appearance, which takes 1.7 million dollars without extra desulphuriser expenses, based on 10MW engine flue gas treatment. The next is the Mg-based system, which cost 2 million dollars in CapEx and $ 1200/year in OpEx for the desulphuriser. NaOH uses about 2.5 million dollars for construction and $ 30000/year in desulphuriser. As for the energy aspect, the seawater and Mg-based systems use less non-renewable energy than the NaOH system in the construction phase. In conclusion, the seawater system shows the best performance and could be an alternative in SOx control technologies. This study sheds light on the comprehensive evaluation of marine environmental protection technologies for further optimisation.