This paper's research objective is to investigate an independent ship with wind-solar-diesel-battery hybrid energy using real-time variations of energy source components in energy storage systems. The costs of fuel, and sewage and real-time output cost of a diesel generator set and energy storage system are also considered. Firstly, this paper investigates the critical output point of energy storage systems under a dynamic load, to determine the priority of energy storage control strategy. Secondly, this paper investigates the issue of power supply optimisation. A three objective optimisation design model is proposed, which includes the cost of the whole life cycle of the system, the microgrid capacity loss and the pollutant treatment cost. This paper also uses the NSGA-II algorithm which is used to investigate the numerous aspects of independent ship microgrid optimisation, while influencing different power combinations and energy control strategies. The results show that the method is accurate and effective.