This study has investigated the effect of using a waste heat recovery system and carbon capture process on carbon reduction efficiency and the Energy Efficiency Design Index (EEDI) to reduce carbon emissions from ships. Organic Rankine Cycle (ORC) was used as waste heat recovery and ORC system turbine power was determined at variable engine loads. The effect of system parameters such as exhaust absorber inlet temperature, MEA concentration and flow rate, number of columns on carbon capture performance has been revealed in the carbon capture process. Furthermore, the EEDI was estimated using the existing system, the ORC system configuration, and the utilization of the carbon capture system. It has been determined that the optimal exhaust absorber inlet temperature is 50 degrees C and the carbon capture performance is 95% on average. In the applied system, the EEDI is reduced by 14% with the ORC system and by 90% with the carbon capture system. ORC system turbine output power ranges from approximately 414 kW to 606 kW for variable CCS inlet temperatures for 100% load condition. Thus, the study predicts that the carbon capture system can effectively meet the regulations in case of using fossil fuels in the future.