The morphology manipulation of nanomaterials by ion irradiation builds a way to precisely control physicochemical properties. Under the continuous irradiation of low energy Ga⁺, Ne⁺, and He⁺ ions, an ion compaction effect has been found in hollow FePt nanochains with ultrathin shell that the volumes of the nanochains are gradually compacted by ions. The deep learning algorithm has been successfully applied to automatically and precisely measure average sizes of spheres in hollow FePt nanochains. The compaction under ion irradiation is very fast in the very early period and then proceeds to a slow region. The compaction rates in both regions are linearly fitted and all the values are in the order of 10^–17 to 10^–14 cm²/ion. Ion species and ion current have effect on the compaction rate. For example, the compaction rate of Ga⁺ ions is larger than those of Ne⁺ and He⁺ ions under an identical current, while irradiation with larger current can compact nanochains faster. The ion compaction effect originates from the local shear deformation caused by the interaction between incident ions and the electrons of Fe and Pt atoms in the ultrathin shell. With continuous irradiation, the crystalline clusters of FePt nanchains firstly grow larger and then become amorphous. The ion compaction effect can be applied to tune the size and crystal structure of hollow structures with a precise rate by choosing appropriate ion species and current.