The advancement of thin, lightweight, and high-power electronic devices has increasingly exacerbated issues related to electromagnetic interference and heat accumulation. To address these challenges, a spray-drying-sintering process is employed to assemble chain-like CoNi and flake boron nitride (BN) into hydrangea-like CoNi@BN heterostructure fillers. These fillers are then composited with polydimethylsiloxane (PDMS) to develop CoNi@BN/PDMS composites, which integrate low-frequency microwave absorption and thermal conductivity. When the volume fraction of CoNi@BN is 44 vol% and the mass ratio of CoNi to BN is 3:1, the CoNi@BN/PDMS composites exhibit optimal performance in both low-frequency microwave absorption and thermal conductivity. These composites achieve a minimum reflection loss of -49.9dB and a low-frequency effective absorption bandwidth of 2.40GHz (3.92-6.32GHz) at a thickness of 4.4mm, fully covering the n79 band (4.4-5.0GHz) for 5G communications. Meanwhile, the in-plane thermal conductivity (λ∥) of the CoNi@BN/PDMS composites is 7.31W m-1 K-1, which is ≈11.4 times of the λ∥ (0.64W m-1 K-1) for pure PDMS, and 32% higher than that of the (CoNi/BN)/PDMS composites (5.52W m-1 K-1) with the same volume fraction of CoNi and BN obtained through direct mixing.