Abstract: Objectives Aiming at the increasingly stringent carbon emission control requirements of the shipping industry, this paper conducts research on the energy efficiency, economic performance and operation optimization of the onboard carbon capture system (OCCS) to realize efficient and economical decarbonization of ship exhaust gas. Methods Based on Simulink, a thermo-electric-carbon coupled energy-mass flow model covering the main engine, auxiliary engine, boiler and OCCS of a 14000 TEU large container ship is established. Through fixed-point steady-state simulation and historical voyage simulation, the operation response law of the alcohol amine decarburization process is analyzed, its economic competitiveness compared with alternative technologies is quantitatively evaluated, and a dynamic optimization strategy of capture rate considering working condition differences is proposed. Results The simulation accuracy of the model meets engineering application specifications, and the specific capture energy consumption of the system is non-constant, non-uniform with unbalanced distribution. At the 40% target capture rate, the voyage fuel consumption increment caused by thermal/electrical loads accounts for about 12%/2.5% of the main engine fuel consumption; the net capture effect decreases but still meets the phased emission reduction threshold of the IMO. Under the current EU carbon market, the system payback period is about 3.7 years, with various economic indicators significantly better than the LNG power retrofitting scheme. The differential configuration strategy of capture rate based on main engine load intervals can realize the synergistic improvement of voyage decarbonization benefit and emission reduction compliance, and the RTPSO-PS algorithm has good optimization applicability. Conclusions OCCS has excellent technical and economic feasibility, and the established coupling model and optimization strategy can provide theoretical reference for engineering applications.