Currently, multifunctional microwave-absorbing materials, especially those with thermal conductivity and microwave absorption functions, have excellent application prospects in electronic packaging. In this study, we first used a sacrificial template method to prepare BCNO using biomass carbon as a template. Then, we used an in-situ synthesis method to grow polypyrrole (PPy) on the surface of BCNO to prepare BCNO@PPy with a core-shell structure. The BCNO@PPy composite exhibits a minimum reflection loss (RLmin) of −52.6 dB at a thickness of only 1.94 mm and an effective absorption bandwidth (EAB) of 5.3 GHz (12.7–18 GHz). The excellent microwave absorption can be attributed to the synergistic effect of polarization loss, conductive loss, and partial magnetic loss in the BCNO@PPy (BPPy) composites, and the multi-wall reflection effect of the core-shell structure, as well as the excellent impedance matching of the composites. Notably, BPPy-3 (polypyrrole content of 28.5 wt%) showed a good thermal conductivity enhancement effect on the epoxy resin (EP) when the content of BPPy-3 was 30 wt%. BPPy-3/EP has a thermal conductivity of 1.82 W(m·K)−1, which is 619.5 % higher than that of pure EP. The good thermal conductivity of the composites is attributed to the excellent compatibility of PPy and epoxy resin, as well as the low interfacial thermal resistance between BCNO and PPy. Therefore, this work can provide a reference for the design of materials with both thermal conductivity and microwave absorption functions.