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 −49.9 dB and a low‐frequency effective absorption bandwidth of 2.40 GHz (3.92–6.32 GHz) at a thickness of 4.4 mm, fully covering the n79 band (4.4–5.0 GHz) for 5G communications. Meanwhile, the in‐plane thermal conductivity (λ∥) of the CoNi@BN/PDMS composites is 7.31 W m−1 K−1, which is ≈11.4 times of the λ∥ (0.64 W m−1 K−1) for pure PDMS, and 32% higher than that of the (CoNi/BN)/PDMS composites (5.52 W m−1 K−1) with the same volume fraction of CoNi and BN obtained through direct mixing.