As a subdivision of the hydrogen energy application field, ship-borne hydrogen fuel cell systems have certain differences from vehicle or other application scenarios in terms of their structural type, safety, environmental adaptability, and test verification. The connection method of the ship-borne hydrogen storage cylinder (SHSC) is very important for the hydrogen fuel cell ship, and the structural parameters of the SHSC are particularly important in the hydrogen refueling process. To ensure the safe and reliable operation of the hydrogen-powered ship, research on the filling of the SHSC under different connection modes was carried out during refueling. In our study, a thermal flow physical model of the SHSC was established to research the hydrogen refueling process of the series and parallel SHSCs. The influence of series and parallel modes of the SHSCs on the hydrogen refueling process was explored, and the evolution law of the internal flow field, pressure, and temperature of series and parallel SHSCs under different filling parameters was analyzed by numerical simulation. Our results confirmed the superiority of the parallel modular approach in terms of thermal safety during refueling. The results can supply a technical basis for the future development of hydrogen refueling stations and ship-board hydrogenation control algorithms.