The directional arrangement of two-dimensional thermally conductive fillers can fully exploit their anisotropic advantages and form efficient thermal conduction paths within the composites, thereby significantly improving their thermal conduction efficiency. In this study, “point-surface” hetero-structured boron nitride nanosheets (BNNS)@Ni thermally conductive fillers with magnetic response are synthesized via in-situ growth and high-temperature carbonization. The H-BNNS@Ni/PDMS (BNNS@Ni horizontally arranged in the polydimethylsiloxane (PDMS) matrix) thermally conductive composites are fabricated via magnetic field orientation. When the mass ratio of BNNS to Ni in BNNS@Ni is 8:1 and the mass fraction of BNNS@Ni is 50 wt.%, the in-plane thermal conductivity (λ_∥) of H-BNNS@Ni/PDMS thermally conductive composites reaches 5.50 W/(m·K), which is 27.8 times higher than that of pure PDMS (0.19 W/(m·K)), and is also significantly higher than that of R-BNNS@Ni/PDMS (BNNS@Ni randomly distributed in the PDMS matrix) thermally conductive composites (4.76 W/(m·K)) with the same mass fraction of BNNS@Ni. H-BNNS@Ni/PDMS thermally conductive composites can reduce the operating temperature at full power by 19.2 °C compared to pure PDMS when used for CPU cooling. Meanwhile, H-BNNS@Ni/PDMS thermally conductive composites also exhibit excellent thermal resistance, photothermal conversion performance, and hydrophobicity.