Abstract: With the continuous advancement of aerospace technology, composite structural materials have been increasingly adopted in aircraft structures due to their lightweight advantages. This study investigates the influence of stacking sequences between carbon fiber reinforced polymer (CFRP) and aluminum (Al) plates on the ballistic performance of composite targets against Zr-based amorphous alloy fragments through a combined experimental and numerical simulation. Fragment impact tests were conducted using a 12.7 mm smoothbore ballistic gun, with initial and residual velocities measured to analyze the failure mechanisms of composite targets. Experimental results demonstrate that the stacking sequence of CFRP significantly affects the overall impact resistance. Compared to the CFRP+Al configuration, the Al+CFRP structure exhibits a 9.3% higher ballistic limit. Placing CFRP as the rear face effectively dissipates fragment kinetic energy and mitigates global plastic deformation. LS-DYNA simulations validate the experimental findings, elucidating the anti-penetration characteristics of differently sequenced CFRP+Al composite targets. This research provides critical insights for optimizing protective composite materials in defense applications.