The former work proved that ion irradiation causes the amorphization of the crystalline MoS2 film and leads to the degradation of the lubricating performance. In this work, in order to investigate the influence of irradiation damage on the amorphous structure, MoS2 film with amorphous structure was prepared and ion (Au2+) irradiation experiment was performed with damage level up to 5 dpa. The results show that after irradiation, the short-range order structure in the amorphous MoS2 film is interrupted, and the degree of disorder of its internal atoms increases. With the increase of the irradiation fluence, although the hardness and elastic recovery of the film increases significantly, the wear lives of the film reduce by two third. Further friction interface analyses reveal that the irradiation damage MoS2 film formed less reordered transferred layer at counter face, which leads to the higher friction coefficient and the shorter wear life.