Despite the ever-increasing demand of nanofillers for thermal enhancement of polymer composites with higher thermal conductivity and irregular geometry, nanomaterials like carbon nanotubes (CNTs) have been constrained by the nonuniform dispersion and difficulty in constructing effective three-dimensional (3D) conduction network with low loading and desired isotropic or anisotropic (specific preferred heat conduction) performances. Herein, we illustrated the in-situ construction of CNT based 3D heat conduction networks with different directional performances. First, to in-situ construct an isotropic percolated conduction network, with spherical cores as support materials, we developed a confined-growth technique for CNT-core sea urchin (CNTSU) materials. With 21.0 wt.% CNTSU loading, the thermal conductivity of composites reached 1.43 ± 0.13 W/(m·K). Secondly, with aligned hexagonal boron nitride (hBN) as an anisotropic support, we constructed CNT-hBN aligned networks by in-situ CNT growth, which improved the utilization efficiency of high density hBN and reduced the thermal interface resistance between matrix and fillers. With ~ 8.5 wt.% loading, the composites possess thermal conductivity up to 0.86 ± 0.14 W/(m·K), 374% of that for neat matrix. Due to the uniformity of CNTs in hBN network, the synergistic thermal enhancement from one-dimensional (1D) + two-dimensional (2D) hybrid materials becomes more distinct. Based on the detailed experimental evidence, the importance of purposeful production of a uniformly interconnected heat conduction 3D network with desired directional performance can be observed, particularly compared with the traditional direct-mixing method. This study opens new possibilities for the preparation of high-power-density electronics packaging and interfacial materials when both directional thermal performance and complex composite geometry are simultaneously required.