As the international LNG trade market is booming, the LNG carrier fleet has expanded year after year. How to reduce energy consumption in boil-off gas (BOG) re-liquefaction process and CO2 generated during transportation has become a hot topic. This paper obtains ideas from the LNG cold energy contained in LNG carriers, and proposes a novel BOG-ORC-CCS system for direct BOG re-liquefaction, Organic Rankine cycle (ORC) and carbon capture and storage (CCS). The BOG-ORC-CCS system recycles waste heat from the ship while realizing the LNG cold energy gradient utilization. The reference ship (Q-Flex) is specified under the framework of Energy Efficiency Design Index (EEDI) phase Ⅲ requirement and the BOG-ORC-CCS system is simulated by Aspen HYSYS software. A comprehensive evaluation of the system performance is carried out under the guidance of energy, exergy, economic and environment (4E) modeling. The results of the 4E analyses show that the proposed BOG-ORC-CCS system has the advantage of low energy consumption and good economic performance. Finally, a multi-objective optimization of the system performance in 4E aspects: system energy and exergy efficiency (ηen,sys×ηex,sys), payback period (PBP) and primary energy saved (PES) are carried out by the third-generation non-dominated sorting genetic algorithm (NSGA-Ⅲ). As a result, the optimal solutions are as follows: ηen,sys is 50.91%, ηex,sys is 54.00%, PBP is 1.55 years and PES is 1.32 MWh, while Load of 75%, TL5 is −136.01 °C, pB5 is 1.82 MPa and ScrL2 is 99.88%. Additionally, SEC is 0.20 kWh/kg, which is much lower than that of conventional indirect re-liquefaction. This demonstrates the feasibility of the BOG-ORC-CCS system on LNG carriers.