Aluminum alloy is the main structural material of research reactors at home and abroad. In this paper, on the basis of the research on the irradiation damage of the structural material aluminum alloy in the 300# research reactor, the microstructural damage and hardness change caused by ion irradiation in 6061-Al alloy are studied to carry out the early exploration of the damage effect of 6061-Al alloy under higher neutron irradiation doses. The results show that 1/3<111> dislocation loops with angles of 72° are generated in 6061-Al alloy after self-ion irradiation. The defect density increases obviously with the increasing irradiation dose from 0.218×10¹⁶ cm^-2 to 4.367×10¹⁶ cm^-2. However, the selected area electron diffraction shows a good lattice structure and no amorphous transformation occurs. Nano-indentation test demonstrates obvious irradiation hardening after irradiation and the microhardness increases with the increasing doses. At the highest damage dose of 2.183×10¹⁶ cm^-2 and 4.367×10¹⁶ cm^-2, the hardening reaches saturation, approaching 11%. These results can provide data support for the preliminary prediction of the structure and property change in 6061-Al alloy under high neutron irradiation dose.