Synergistic design of rational heterogeneous interface structure and magnetic components can effectively regulate and enhance the polarization loss and magnetic loss capacity of metal-organic frameworks (MOFs) derived magnetic carbon-based composites, thereby improving their microwave absorption performance with low thickness and broad absorption bandwidth. In this work, a novel two-dimensional core-shell structured Co@C/Fe composites were fabricated through the deposition of Fe on bimetallic flaky Co/Zn MOFs, followed by thermal decomposition. Results revealed that the pyrolysis temperature has a significant impact on the composition, morphology, magnetic properties, and microwave absorption performance of the as-obtained composites. After pyrolyzing at 700 °C, the flaky core-shell structured Co@C/Fe composites exhibit excellent microwave absorption performance. Specifically, the minimum reflection loss can reach -86.15 dB with an ultrathin thickness of 1.38 mm, and the effective absorption bandwidth can extend to 5.1 GHz at a low thickness of 1.51 mm. The introduction of the core-shell structure and the magnetic Fe shell played critical roles on the enhanced microwave absorption performance. It is believed that this work may offer a new paradigm and approach for the preparation of ultrathin and high-performance MOFs-derived microwave absorption materials, thereby expanding the application scope of MOFs.