The increase of ship’s energy utilization efficiency and the reduction of greenhouse gas emissions have been high lightened in recent years and have become an increasingly important subject for ship designers and owners. The International Maritime Organization (IMO) is seeking measures to reduce the CO2emissions from ships, and their proposed energy efficiency design index (EEDI) and energy efficiency operational indicator (EEOI) aim at ensuring that future vessels will be more efficient. Waste heat recovery can be employed not only to improve energy utilization efficiency but also to reduce greenhouse gas emissions. In this paper, a typical conceptual large container ship employing a low speed marine diesel engine as the main propulsion machinery is introduced and three possible types of waste heat recovery systems are designed. To calculate the EEDI and EEOI of the given large container ship, two software packages are developed. From the viewpoint of operation and maintenance, lowering the ship speed and improving container load rate can greatly reduce EEOI and further reduce total fuel consumption. Although the large container ship itself can reach the IMO requirements of EEDI at the first stage with a reduction factor 10% under the reference line value, the proposed waste heat recovery systems can improve the ship EEDI reduction factor to 20% under the reference line value.