Thermal management is of importance to microelectronic industry. Owing to both excellent thermal conduction and electrical insulation, hexagonal boron nitride (BN) platelets are the widely-used thermal conductive fillers in polymers. Adding high content of BN can endow polymers high thermal conductivity, but in most cases, destroy the flexibility, failure strength as well as processability of the polymers significantly. Here, we report a multi-material 3D printing technique to prepare high thermal conductive epoxy based composites, by which BN platelets were assembled together in heat-conducting phase to form the dense, continuous thermal pathway. The BN platelets show excellent alignment along printing direction in epoxy matrix due to the shear-inducing effect of printing. The composites at filler loading of 20 wt% exhibit the thermal conductivity of 2.52 W·m−1·K−1 along printing direction. The thermal conductivity of the composites is in good agreement with the prediction of parallel model. It indicates that the composites with specific thermal conductivity can be prepared by tailoring the printing ratio of the heat-conducting phase to the matrix phase. Mechanical and insulating performance of the composites maintain good enough as well.