Mn52Bi48 (15 nm) and Mn54Bi24Cu21 (15 nm) thin films were prepared by the magnetron sputtering and vacuum annealing at 350 °C, and the variations of their structures and magnetic properties with 30 keV Kr+ ion irradiation were studied. The MnBi and MnBiCu films exhibited saturation magnetizations Ms of 180 emu/cc and 210 emu/cc, the coercivities Hc of 10 kOe and 3.4 kOe, respectively. The Ms and Hc of the MnBi abruptly vanished by the irradiation of ion dose at 3 × 1014 ions/cm2, while those of the MnBiCu film gradually decreased with increasing the ion dose and became zero at 5 × 1013 ions/cm2. The different trend on the ion irradiation between MnBi and MnBiCu films is understood by the surface structure of the film, i.e., the MnBi has convex islands on its surface, which protect the underneath NiAs-type MnBi from the irradiation, while the MnBiCu has rather flat surface, and its crystal structure was uniformly modified by the irradiation. From the surface flatness and the uniformity of the MnBiCu film, as well as the low annealing temperature of 350 °C, it was concluded that the MnBiCu film is one of the attractive materials for high-density ion irradiation bit patterned media.