Poor impedance matching and a single loss mechanism are typical challenges for carbon-based materials to become efficient microwave absorbers. To address these issues, defect introduction and interfacial strategies are effective methods for enhancing microwave absorption through the micro-mechanism of material interaction with microwaves. Additionally, forming a homogeneous composite material is crucial for achieving good impedance matching. In this study, we used a controlled solvent-thermal method to achieve self-assembled interfacial intercalation, yielding amorphous VOPO4/rGO nanohybrids, which show significantly enhanced microwave absorption properties. The abundant defects introduced by VOPO4 within the amorphous layered composites disrupt the charge distribution, contributing to polarization loss. The graphene nanosheets expose more VOPO4 structural units, facilitating increased conductivity and enriching the microwave absorption mechanism. As a result, the prepared VOPO4/rGO nanohybrids demonstrate outstanding microwave absorption, with the effective absorption bandwidth covering the entire Ku-band (11.6–18.0 GHz) at a thickness of 2.3 mm. This research provides an important reference for understanding the mechanisms that enhance the electromagnetic wave absorption of carbon-based materials.