Carbon fiber reinforced polymer (CFRP) composites are promising lightweight structural materials in high-tech areas such as aerospace engineering which require both mechanical reliability and electromagnetic interference (EMI) shielding capability. Their EMI shielding is reflection-dominated mainly owing to their good electrical conductivity, but inevitable low-velocity impact during service would damage their structural integrity and disrupt conductive networks, leading to significantly degraded or unstable EMI shielding performance. In this study, a rigid-flexible structural strategy is proposed by incorporating a functional rubber (F-rubber), formulated as Fe₃O₄@MWCNTs/rubber (FMR), either between CFRP layers (symmetric CFRP/FMR) or on the surface of CFRP (asymmetric CFRP/UFMR). Both configurations outperform pristine CFRP in EMI shielding, impact energy dissipation, and post-impact shielding performance, while the FMR layer position determines their dominant advantage. The surface integrated CFRP/UFMR improves impedance matching and electromagnetic absorption, achieving absorption-dominated shielding with a total shielding effectiveness of approximately 40 dB. Internally embedded CFRP/FMR provides more effective impact buffering and conductive network protection, retaining approximately 96% of its initial shielding effectiveness after impact. These results establish a position-dependent design principle: surface placement favors absorption-oriented shielding, whereas internal placement enhances post-impact functional stability, providing a practical route to lightweight multifunctional aerospace composites.