The reasonable design of magnetic carbon-based composites is of great significance to improving the microwave absorption (MA) performance of the absorber. In this work, ultrafine FeNi3 nanocrystals (5–7 nm) embedded in a 3D honeycomb-like carbon matrix (FeNi3@C) were synthesized via a facile strategy that included a drying and carbonization process. Because of the soft magnetic property of the FeNi3 nanocrystals and their unique 3D honeycomb-like structure, the FeNi3@C composites exhibit excellent MA abilities. When the filler loading ratio of FeNi3@C/paraffin composites is only 30 wt%, the maximum reflection loss (RL) value is −40.6 dB at 10.04 GHz. Meanwhile, an ultra-wide absorption frequency bandwidth of 13.0 GHz (5.0–18.0 GHz over −10 dB) can be obtained in the thickness range of 2.0–4.5 mm, and this means that the absorber can consume 90% of the incident waves. It benefits from the dual loss components, multiple polarizations, and multiple reflections for improving MA performances of FeNi3@C composites. These observations suggest that the 3D honeycomb-like FeNi3@C composites have broad application prospects in exploring new MA materials that have a wide frequency bandwidth and strong absorption.