Three-dimensional (3D) porous molybdenum disulfide nanosheets/carbon nanofibers (MoS2/CNF) hybrid aerogels were synthesized by using solvothermal method and following carbonization, where two-dimensional (2D) MoS2 nanosheets were homogenously in-situ grown on the interconnected CNF skeleton derived from bacterial cellulose, forming a hierarchical porous structure. This unique heterogeneous structure of the MoS2/CNF hybrid aerogels were conducive to electromagnetic loss, including conduction, polarization, multi-scatterings, and reflections, thus resulting in a balanced impedance matching and microwave attenuation capacity. It was found that the resulted MoS2/CNF hybrid aerogels demonstrate excellent microwave absorbing performance when the only 5.0 wt% fillers were loaded in paraffin. Particularly, MoS2/CNF-2–900 hybrid aerogel displayed an effective absorption bandwidth of 5.68 GHz and minimum reflection loss (RLmin) value of −36.19 dB at a thickness of 2.0 mm. As the thickness increases to 4.4 mm, the RLmin value of MoS2/CNF-2–900 hybrid aerogel reaches −48.53 dB. Electromagnetic loss mechanism analysis indicates that such improved microwave attenuation is attributed to proper component, multiple heterogenous interface and hierarchical porous structures. All the results in this work pave the avenue for the development of ultralight microwave absorber with high absorption capacity as well as broad effective absorption bandwidth.