Greenhouse gas emissions from maritime activities are increasing and threatening the world. To limit greenhouse gas emissions, the International Maritime Organization (IMO) has taken decisions at a level that pushes the techno-economic limits of the maritime sector and has started to put these decisions into effect in various phases. With a huge CO2 reduction potential of up to 90%, carbon capture and storage (CCS) systems offer a feasible solution for reducing CO2 emissions for various ship types and meet IMO’s regulations on greenhouse gas emissions. In this study, the effects of using several innovative ionic liquids as a solvent on the CO2 capture performance and cost of CCS systems were investigated to make CCS systems even more feasible. The ionic liquids were synthesized following the literature and verified by Fourier transform infrared spectroscopy analysis. When the [TMG][Im] ionic liquid is compared with the 30 wt% aqueous monoethanolamine (MEA) solution, which is widely used in CCS systems, it is found that the ionic liquid dissolved about 435.6% higher CO2 in the first 5 min. In a CCS system using a 30% aqueous MEA solution, a 6.5-m-long column is required for a Q-Flex type vessel according to the literature. However, in this study, it is estimated that using the 1,1,3,3-tetramethylguanidinium imidazole ([TMG][Im]) ionic liquid would meet the requirement with a 4.75-m-long column, reducing the column cost by 26.9% accordingly. Although the use of [TMG][Im] increases the load on solvent pumps due to increased viscosity, this increase in pump power accounts for only 0.3% of the total power requirement of the CCS system.