Polymer nanocomposite (PNC) with high thermal conductivity and excellent mechanical performance show great potentials in a broad of engineering fields, such as electronic industry, flexible electronics, and phase changing materials. In particular, PNC has been widely used as thermal interfacial materials in advanced electronics [1], which desires a high thermal conductivity. However, pristine PNC has a low thermal conductivity of around 0.2 W/mK. As such, extensive works have been carried out to find out effective ways in improving its thermal transport properties. Based on molecular dynamics simulations, this work assesses the thermal transport in polyethylene (PE) nanocomposites with the presence of a new one-dimensional (1D) nanofiller – carbon nanothread (NTH). Carbon nanothread is a novel ultrathin 1D carbon nanostructure, with all C atoms in sp³ bonds. It has been reported with tunable mechanical [2] and thermal properties [3], and appealing applications for carbon nanofibers [4] and nano-scale mechanical energy storage devices [5]. In this work, we found that the increasing content of regularly aligned NTH fillers will improve the axial thermal conductivity of the PE nanocomposite increases. However, the aggregated NTHs are found to degrade the enhancement effect. Specifically, the randomly dispersed NTHs can hardly promote the heat transfer due to the lacking of effective heat transfer channels within the PE matrix. Moreover, surface functionalization is found to introduce an adverse effect on the thermal conductivity due to the existence of additional voids. The formation of voids explain a long-standing open question that functionalization of the heat conductive filler only slightly improve the thermal conductivity of the polymer composite. This work provides an in-depth understanding of the heat transfer within the polymer nanocomposites, which opens up space for the preparation of highly conductive polymer.