Optimizing ship operations in the maritime industry is crucial for enhancing efficiency and sustainability. With the increasing emphasis on reducing carbon emissions and fuel consumption, innovative solutions are needed to address these challenges. The multi-objective ship operations optimization decision support system (MSODSS) aims to improve the efficiency and sustainability of ship operations by integrating advanced simulation-based optimization algorithms and considering inputs such as power sources, equipment health, route, navigation, and weather data. This paper presents the development of an MSODSS prototype based on the FlexSim simulation system. The MSODSS system architecture, data sources, and simulation model are discussed, and a case study for comparing ship operations in different weather conditions is used to demonstrate the system's functionalities. Preliminary results indicate that a significant increase in fuel consumption and carbon emissions may occur with even modest increases in ship speed.