The hydrogen fuel powered ship in navigation interacts with the surrounding ships, shore constructions and people. Therefore, it is necessary to assess the ship safety during navigation. This article selects the hydrogen fuel powered ship which will sailing in Yangtze River as research object to study the ship risks in navigation and assess the consequences of accidents. Jet flame accident and flash accident are two main accident scenarios that may occur during the sailing of hydrogen fuel cell powered ships. Based on the HyRAM software, the flame size, thermal radiation range and fatality rate of the ship under these two scenarios are quantitatively analyzed, and the sailing risk of the ship is quantitatively assessed. The risks of the hydrogen fuel powered ship in navigation is evaluated quantitatively by calculating the personal risk and determine the risks which can be accepted by crew, passengers on board and people on shore.