In this paper, three mainstream carbon capture technologies for vessel emissions, including MEA method, ammonia method and membrane separation method, are compared and studied. According to the research results, MEA method is mature, but it has high energy consumption and corrosion problems; ammonia method has obvious advantages in absorption efficiency and cost, but its risk of ammonia escape needs to be controlled; membrane separation method is characterized by low energy consumption and compact structure, but it is limited by material properties. The economic analysis shows that when the carbon price exceeds 150 USD/ton, membrane separation method and ammonia method are better than MEA method in terms of comprehensive benefits. It is worth noting that environmental conditions significantly affect technical performance. For example, when operating in high-humidity sea areas, the efficiency of membrane separation method will decrease by 10–15%, and energy consumption compensation needs to be increased. Based on the research results, it is suggested that the key development directions in the future include developing multi-technology coupling scheme to play a synergistic effect, establishing targeted policy incentive mechanism, and optimizing the scheme of integration with ship power system, so as to advance the commercial application of onboard carbon capture, utilization and storage (CCUS) technology.