Simultaneously achieving excellent shielding effectiveness (SE) and high absorption rate of flexible electromagnetic interference (EMI) shielding materials has become a growing demand for the new generation of highly integrated electronic devices. This study constructed a double-layer polydimethylsiloxane (PDMS) EMI shielding composite film, with the upper layer using Ni-plated carbon fiber (Ni@CF) as the high absorption loss part and the lower layer using Ag-plated graphene fiber (Ag@GF) as the reflection attenuation part. Due to the synergistic magnetic/dielectric loss effect in the upper layer, high electrical conductivity in the lower layer, and the shielding mechanism of “absorption-reflection-reabsorption” induced by the double-layer structure, this composite film achieves efficient EMI shielding performance and high absorption characteristics in the X-band. The EMI SE values of the 2 mm thick film containing 0.03 wt% Ni@CF and 1.2 wt% Ag@GF reach 33.7 dB, while shielding effectiveness of reflection (SER) and absorption (SEA) is 0.8 dB and 32.9 dB, respectively. This result means that the composite film only reflects 17.2 % of the microwaves while shielding 99.9 % and absorbs nearly 82.7 %, exhibiting a significant absorption-dominated shielding mechanism. This flexible and efficient shielding film with a high absorption rate suits portable and wearable intelligent electronic products to reduce secondary electromagnetic pollution.