Hydrogen bubble phenomenon is one of the key issues to be solved in the development of a long-life target system for boron neutron capture therapy (BNCT). In this study, we assessed the kinetic behaviors of H impurities in the nano-composite target from the atomic level. Firstly, two kinds of Li/Ta nanolayer models were constructed, based on the calculated lattice parameters and surface energies. The H solution energy, diffusion mechanism, and hydrogen bubbles formation in the Li/Ta nanostructured bilayer were studied, through theoretical modeling and simulation. Our results show that the Li/Ta interfaces are effective sinks of H atoms because the H solution energies in the interface are lower. Meanwhile, due to the relatively low diffusion barriers, the large-scale H transport through the interface is possible. In addition, although it is more likely to form hydrogen bubbles in the Ta layer, compared with the Li layer, the anti-blistering ability of Ta is more impressive compared with most of other candidate materials. Therefore, the Ta layer is able to act as the hydrogen absorber in the Li/Ta bilayer, and relieve the hydrogen damage of the Li layer in the large-scale proton radiations.