The need for supplying eco-friendly ships such as hydrogen ships is increasing as a response to the strengthened environmental regulations of the IMO and to achieve 50% of the greenhouse gas reduction target in 2050. Hydrogen is an eco-friendly fuel that does not emit harmful gases and can be directly burned or converted into high-efficiency electric energy by using it as a fuel cell. However, despite these advantages, hydrogen has a wide combustion range of 4 to 75 vol% and has low ignition energy of 0.02 mJ, so that it is easily ignited by static electricity, etc., and is highly likely to lead to an explosion. In particular, ships have specificities due to structural and environmental characteristics, which act as factors affecting hydrogen diffusion characteristics. However, there is a limit in the fact that these characteristics are not reflected in the research conducted so far and the current regulations to ensure safety in case of leakage of hydrogen ships. Therefore the purpose of this paper is to propose major factors influencing the shape, ventilation method, and gas detector position selection considering the structural and environmental characteristics of ships and hydrogen fuel characteristics for effective ventilation and leakage detection. To achieve this, first, an experiment was performed for the analysis of the hydrogen leakage and diffusion characteristics due to the ship motion, and the result of the hydrogen concentration for each sensor obtained through this was expressed as a formula with respect to time. In addition, the necessity of improving ventilation performance and factors affecting the location of gas detectors were suggested. Second, the shape and ventilation method according to the ceiling apex angle of the hydrogen fuel storage area were proposed and the ventilation performance improvement effect was analyzed. Third, the fire damage reduction effect according to the ventilation improvement plan was analyzed. As a result, it was confirmed that when the direction of hydrogen leakage is longitudinal, the hydrogen diffusion characteristics are affected by pitch motion, and the difference in hydrogen concentration is about twice as large in pitch motion compared to roll motion. For this reason, it was confirmed that it is necessary to propose a shape and ventilation method that can minimize the difference in concentration values depending on the ship motion. Also, when selecting the location of the hydrogen gas detector, it was confirmed that the location where hydrogen can be accumulated varies depending on the direction, location, and movement of hydrogen leakage. In addition, it was confirmed that when the hydrogen fuel storage area is located on the open deck or in the closed area, natural ventilation or mechanical ventilation is effective in terms of ventilation performance and fire damage reduction when the roof apex angle is 120°. In the future, it is judged that the above research results can be used for predicting hydrogen concentration according to the ship motion period and it is expected that it can be used as reference data when designing the hydrogen fuel storage area.