To enhance the electromagnetic shielding performance of traditional electromagnetic shielding materials, a layer-by-layer filtration technique was employed to incorporate zinc powder, silver powder, and lanthanum oxide into carbon nanotubes, resulting in MWCNTs/Zn, MWCNTs/Ag, and MWCNTs/La2O3 interlayer materials. The study investigated the effects of different doping levels on the microstructure, electrical conductivity, and electromagnetic shielding performance of the hybrid carbon paper. The research found that the introduction of nanoparticles significantly altered the microstructure of the carbon paper. When the content increased to 20 wt%, all three fillers began to fill the interlayer pores and form a continuous structure. Zn formed a band-like enrichment in the middle layer, Ag formed a continuous chain network along the axis of the carbon nanotubes, and La2O3 was embedded in clusters within the interlayer pores. After doping, Zn and Ag exhibited single-metal crystal diffraction peaks, with peak intensity increasing as the doping level increased. Doping with La2O3 caused the (002) peak of the carbon nanotubes to shift to a higher angle, 26.28°. After doping with Ag, the system’s electrical conductivity increased to 40.3 S/cm. Electromagnetic shielding tests showed that when the filler content exceeded 20 wt%, the shielding performance declined due to agglomeration. However, the Ag system maintained a high shielding level of 66.6 dB due to its particle shear rearrangement characteristics. These structural-property correlations provide a theoretical basis for the controllable preparation of lightweight electromagnetic shielding materials.