High-efficiency microwave absorption epoxy nanocomposites filled with ultralow content of non-covalently modified reduced graphene oxides (rGO) are prepared via an in-situ polymerization method. Here, the porous and folded rGO nanosheets are successfully functionalized by strong π-π interaction between conjugated imidazole and graphene sheets. The combination of electron microscope and synchronous radiation X-ray small angle scattering (SAXS) techniques unambiguously illustrates that the non-covalently modified graphene nanosheets in the epoxy composites are well-dispersed and extensively winkle. Hence, compared with pristine rGO/epoxy composites, the composites containing the highly dispersed rGO demonstrate more ideal impedance matching and stronger microwave dissipation based on the experimental and simulated results. The composites remarkably achieve excellent microwave absorptions (minimum reflection loss of −65 dB, with a matching thickness of 1.8 mm), an extremely broad absorbing bandwidth of 7.48 GHz (RL < −10 dB) and ultralow filler loading (1–2 wt%). Moreover, the composites possess high hydrophobicity, endowing them attractive functions of self-cleaning. This work provides a promising, facile and scalable approach for designing and fabricating graphene-based nanocomposites with hydrophobicity and excellent microwave absorption capacities.