The photovoltaic system is widely introduced into ocean-going ships to utilize the abundant solar resources on the ocean, reduce the ship's fuel consumption and pollutant emission. As the uncertainty of navigation environment, ship's attitude and climate conditions, the dynamic partial shading or even complex illumination conditions probably occur during the long time voyage. In this paper, a large-scale photovoltaic (PV) system is introduced into the ocean-going green ship to modify the traditional structure of ship's power grid. Specifically, a novel structure of large-scale PV array based on the ship's illumination unit (SIU), ship's photovoltaic group (SPG), operating point controlling device (OPCD) and batteries is proposed, and layout of the array on oceangoing green ship is researched as well. Besides, the MPPT of all the SIUs is modeled as a large-scale global optimization (LSGO) problem, and a meta-heuristic optimization called the DCDE is employed to solve this problem offline. Performance of the DCDE is verified by numerical experiments, and result of simulation also shows that with the application of the proposed structure and its controlling methods, the green ship can make full use of solar resources and achieve its operational safety and efficiency under complex environmental conditions.