By using pulse electrodeposition, a copper nanopillar array (CuNPA) was filled into porous anodized aluminum oxide (AAO) films to achieve a highly thermal conductive interconnector with anisotropic property. After 120 min pulse deposition, CuNPA uniformly filled the pores of AAO with a pore-filling percentage of 99.4%, as the ion concentration in AAO pores can re-equilibrate to electrolyte concentration during the current-off period. The CuNPA-filled AAO film showed a high thermal conductivity of 153.12 W/(m·K) in the vertical direction and a low thermal conductivity of 3.43 W/(m·K) in the horizontal direction. Hence, the anisotropic ratio of the thermal conductivity reached 44.64. Moreover, the fabrication process was facile and cost-effective, showing a potential application prospect in the field of high-density packages and power electronic devices.