This study details microwave-absorbing materials made of natural rubber/nitrile butadiene rubber (NR/NBR) blends with multi-walled carbon nanotubes (MWCNTs) and molybdenum disulfide (MoS2). The mechanical blending method and the influences of fabrication on the morphology and microwave-absorbing performance of resulting compounds were logically investigated. It was found that interfacial differences between the fillers and matrix promote the formation of MWCNTs and MoS2networks in NR/NBR blends, thus improving microwave-absorbing performance. Compared with direct compounding, masterbatch-based two-step blending is more conducive to forming interpenetrating networks of MWCNTs/MoS2, endowing the resulting composite with better microwave attenuation capacity. Composites with MWCNTs in NR and MoS2in NBR demonstrate the best microwave-absorbing performance, with a minimum reflection loss of −44.54 dB and an effective absorption bandwidth of 3.60 GHz. Exploring the relationship between morphology and electromagnetic loss behavior denotes that such improvement results from the selective distribution of dual fillers, inducing networking and multi-component-derived interfacial polarization enhancement.