The Maritime Labour Convention (2006) demands the improvement of the ship living environment. The lighting system with the widest coverage of the working and living environment on board has been studied in order to improve the ship environment. A human factors design method of the ship lighting system is proposed according to the optical biological effect theory, with detailed design procedures. The feasibility of the design method is proved based on the design process of a full-scale ship. This proposed design method can optimize the ship lighting system design and improve the seafarer's working and living environment.