In recent years, the application of solar energy and energy storage to ship power systems has shown promise as a method for both reducing annual carbon and nitrogen oxide emissions and improving ship energy efficiency in the maritime shipping industry. When a ship navigates at sea, it encounters a constant rocking motion that is affected by both the surrounding sea conditions and the ship’s navigation parameters. This motion increases the uncertainty involved in using solar energy and accelerates the aging of the ship’s energy storage battery to some extent. In this study, a universal mathematical model is established for the power generation by photovoltaic (PV) modules in which both the sea conditions and the ship’s integrated motion, including its basic movement along with the motion caused by rocking, are taken into account. Based on this model, the fluctuation characteristics of a ship’s PV output power are studied and determined using three different simulation scenarios. A binary energy storage scheme based on a decoupled PV output power is proposed in order to both stabilize the small-period PV power fluctuations and slow the aging of the actual battery caused by rocking. In addition, a super-capacitor (SC) configuration is constructed based on a maximum half cycle. Finally, the optimal energy storage capacities for this green ship are compared under both rocking and moving motion. In the case of rocking motion, the SCs are able to achieve an approximately 24.8–35.0% reduction in battery replacement. A shipping route between Shanghai, China and Sydney, Australia is considered to validate the practicality of implementing the proposed method.