Abstract The microstructure design for thermal conduction pathways in polymeric electrical encapsulation materials is essential to meet the stringent requirements for efficient thermal management and thermal runaway safety in modern electronic devices. Hence, a composite with three-dimensional network (Ho/U-BNNS/WPU) is developed by simultaneously incorporating magnetically modified boron nitride nanosheets (M@BNNS) and non-magnetic organo-grafted BNNS (U-BNNS) into waterborne polyurethane (WPU) to synchronous molding under a horizontal magnetic field. The results indicate that the continuous in-plane pathways formed by M@BNNS aligned along the magnetic field direction, combined with the bridging structure established by U-BNNS, enable Ho/U-BNNS/WPU to exhibit exceptional in-plane ( λ // ) and through-plane thermal conductivities ( λ ⊥ ). In particular, with the addition of 30 wt% M@BNNS and 5 wt% U-BNNS, the λ // and λ ⊥ of composites reach 11.47 and 2.88 W m −1 K −1 , respectively, which representing a 194.2% improvement in λ ⊥ compared to the composites with a single orientation of M@BNNS. Meanwhile, Ho/U-BNNS/WPU exhibits distinguished thermal management capabilities as thermal interface materials for LED and chips. The composites also demonstrate excellent flame retardancy, with a peak heat release and total heat release reduced by 58.9% and 36.9%, respectively, compared to WPU. Thus, this work offers new insights into the thermally conductive structural design and efficient flame-retardant systems of polymer composites, presenting broad application potential in electronic packaging fields.