Abstract: Boron neutron capture therapy (BNCT) is a biologically-targeted radiotheraphy method that can selectively block cancer cells. The application of this treatment method in medical ship is based on IAEA cancer care project, aiming to provide cancer medical assistance and other medical services for developing countries in Africa or other continents. Neutron irradiation theraphy module of the ship was introduced in this paper, and the module was based on the design prototype of in-hospital neutron irradiator-1 (IHNI-1) built in China. According to the requirements of special environment and condition of marine reactor, the shape of reactor pool, the selection of shielding material, the structure of reactor complex system and equipment and the general layout of neutron irradiation theraphy module were optimized. The analysis shows that the design concept and scheme have some development value and application feasibility.