The production of magnetic biomass-derived carbon-based aerogels has made outstanding contributions to green chemistry and sustainable development so as to alleviate the growing electromagnetic pollution problems. In particular, carboxymethyl cellulose (CMC) possessing three-dimensional (3D) porous structure, low density and biodegradability is an effective precursor for the preparation of magnetic carbon aerogels. In this work, lightweight porous Fe3O4-Fe/carbon aerogels (FFCA) were synthesized by depositing magnetic metals on chitosan (CS)-reinforced CMC via a facile and eco-friendly strategy. The 3D porous structure and non-homogeneous conductive network endow the FFCA aerogels with comprehensive properties. Specifically, the introduction of magnetic material and the carbonization process under the temperature gradient result in tunable electromagnetic parameters and good impedance matching, allowing electromagnetic waves to enter the absorber and dissipate as much as possible. For instance, the FFCA prepared at 900 °C exhibits the impressive microwave absorption performance due to the synergistic transition between magnetic permeability and dielectric constant, with the minimum reflection loss of −45.5 dB at 2.6 mm and the effective absorption bandwidth of 3.7 GHz. This work provides an important reference for the design of eco-friendly CMC-based magneto-dielectric synergistic microwave absorption materials.