Abstract: To investigate the formation process of the post-target debris cloud generated by Zr-based amorphous fragments and its penetration and damage effects on spaced aluminum targets, a numerical simulation method was developed based on a finite element method-smoothed particle hydrodynamics (FEM-SPH) adaptive coupling algorithm. The reliability of the computational model was verified through ballistic gun tests. Subsequently, numerical simulations were conducted to evaluate the penetration and damage effects of Zr-based amorphous fragments on double-layer spaced aluminum targets under various conditions. The results indicate that, compared with the conventional FEM algorithm, the FEM-SPH adaptive coupling algorithm can more accurately simulate the target-perforation fragmentation of Zr-based amorphous alloy fragments and the associated structural damage effects, with an average calculation error of less than 10%. Variations in the spacing between targets affect the expansion and evolution process of the debris cloud, as well as the damage mode of the rear target. As the spacing increases, the distribution range of the debris cloud expands continuously, and its mass density decreases; correspondingly, the deformation energy of the rear target monotonically increases, while the perforation area initially increases and then decreases. Furthermore, the damage mode of the rear target transitions from penetrative damage dominated by localized shear to structural damage dominated by large plastic deformation.