A neutron capture therapy system capable of eliminating amyloid β-protein includes a neutron capture therapy device and a compound capable of specifically binding to the amyloid β-protein having a nuclide with a large thermal neutron capture cross section. The neutron capture therapy device includes a neutron source, a beam shaping assembly and a collimator, the neutrons released by the neutron source pass through the beam shaping assembly and are slowed into a neutron beam within a certain energy range. The neutron beam irradiates the compound, and the energy generated by the reaction thereof can destroy the structure of the amyloid β-protein. The neutron capture therapy system can specifically eliminate the amyloid β-protein, and reduce the damage to the tissues surrounding the amyloid β-protein.