To clarify the radiation tolerance mechanism of the crystal/amorphous (CA) structure, molecular dynamics (MD) simulations were employed to investigate the plastic deformation and fracture behaviours of nanoscale Cu/CuZr core-shell CA composites and nanocrystalline (NC) Cu, both in the pre- and post-helium (He) irradiation states. Key results demonstrate that regardless of the irradiation condition, the CA structure exhibits superior plasticity and fracture resistance compared to NC Cu. Notably, the mechanical performance of the CA composites is highly dependent on the thickness of the amorphous shell, which directly modulates their response to irradiation. Post-irradiation crack analysis confirms that thicker amorphous layers enhance crack-tip passivation, and this effect remains unimpaired by the presence of He bubbles—an observation that underscores the structural stability of the CA configuration against irradiation-induced defects. With the increase in amorphous shell thickness, the deformation mechanism of the CA composites transitions from the interaction between dislocations and shear transformation zones (STZs) to being dominated by shear banding; this transition correlates with corresponding changes in the material’s strength, plasticity, and deformation characteristics. Collectively, the CA structure exhibits reduced sensitivity to the expansion of He bubbles, which enables its superior crack passivation capability. These findings provide atomic-scale insights and support for the development of radiation-resistant CA materials, holding significant implications for applications in nuclear engineering.