Fe-13Cr-3.5Al-2.0Mo-1.5wt.% ZrC alloy was irradiated by 400 keV Fe+ at 400 °C at different doses ranging from 6.35 × 1014 to 1.27 × 1016 ions/cm2 with a corresponding damage of 1.0–20.0 dpa, respectively, to investigate the effects of different radiation doses on the hardness and microstructure of the reinforced FeCrAl alloys in detail by nanoindentation, transmission electron microscopy (TEM), and atom probe tomography (APT). The results show that the hardness at 1.0 dpa increases from 5.68 to 6.81 GPa, which is 19.9% higher than a non-irradiated specimen. With an increase in dose from 1.0 to 20.0 dpa, the hardness increases from 6.81 to 8.01 GPa, which is an increase of only 17.6%, indicating that the hardness has reached saturation. TEM and APT results show that high-density nano-precipitates and low-density dislocation loops forme in the 1.0 dpa region, compared to the non-irradiated region. Compared with 1.0 dpa region, the density and size of nano-precipitates in the 20.0 dpa region have no significant change, while the density of dislocation loops increases. Irradiation results in a decrease of molybdenum and carbon in the strengthening precipitates (Zr, Mo) (C, N), and the proportionate decrease of molybdenum and carbon is more obvious with the increase in damage.