In this work, we propose novel layer-structured polymer composites (PCs) for manipulating the electromagnetic (EM) wave transport, which holds unique electromagnetic interference (EMI) shielding features. The as-prepared PCs with a multilayered structure exhibits significant improvement in overall EMI shielding effectiveness (EMI SE) by adjusting the contents and distribution of electrical and magnetic loss fillers. The layer-structured PCs with low nanofiller content (5 wt % graphene nanosheets (GNSs) and 15 wt % Fe3O4) and a thickness of only 2 mm exhibited ultrahigh electrical conductivity and excellent EMI SE, reaching up to 2000 S/m and 45.7 dB in the X-band, respectively. The increased EMI SE of the layer-structured PCs was mainly based on the improved absorption rather than the reflection of electromagnetic waves, which was attributed to the “absorb-reflect-reabsorb” process for the incident electromagnetic waves. This work may provide a simple and effective approach to achieve new EMI shielding materials, especially for absorption-dominated EMI shielding.