Because solar energy is intermittent and a ship's power-system load fluctuates and changes abruptly, in this work, the solar radiation parameters were adjusted according to the latitude and longitude of the ship and the change of the sea environment. An objective function was constructed that accounted for the cost and service life simultaneously to optimize the configuration of the marine diesel engine hybrid energy system. Finally, the improved artificial bee colony algorithm was used to optimize and obtain the optimal system configuration. The feasibility of the method was verified by ship navigation tests. This method exhibited better configuration performance optimization than the traditional methods.