The irradiation-induced phase transformation and mechanical property stability of the Cu48Zr48Al4 bulk metallic glass composites (BMGCs) were investigated. An obvious structural transformation occurred from the B2-CuZr phase to the B19′-CuZr and the B33-CuZr phases following irradiation, when the dose increased from 2.5 × 1017 ions/cm2 to 1.0 × 1018 ions/cm2. This change was accompanied by the changes of the maximum displacement per atomic (DPA) increasing from 21.5 dpa to 86 dpa. The mean surface roughness increased as the incident dose increased. The local exfoliation occurred at the maximal dose. The changes of mechanical properties were characterized via nanoindentation. The hardness and Young's modulus in the amorphous regions decreased as the dose increased. In contrast, the crystalline regions presented a distinct hardening effect, due to the appearance of the martensitic phases. The macroscopic hardness of the BMGCs obtained by the Vickers indentation instrument was basically unchanged after irradiation. The results suggested that these materials maintained a stable performance, because of the combined effects of hardening and softening. This study could aid the design of novel materials that are subjected to irradiation circumstance.