Carbon nanotube (CNT)-based networks are promising reinforcements for polymer nanocomposites without the issue of CNT agglomeration. In this study, the CNT junction, a vital and representative structure of CNT-based networks, was applied as the reinforcement of the polyethylene (PE) matrix. The tensile properties of the CNT-junction/PE nanocomposite were investigated via molecular dynamics (MD) simulations and compared with those of pure PE matrix and conventional CNT/PE nanocomposites. The CNT junction was found to significantly increase the mechanical properties of the PE matrix. The Young’s modulus, yield strength, and toughness rose by 500%, 100%, and 200%, respectively. This mechanism is related to the enhanced interfacial energy, which makes the polymer matrix denser and stimulates the bond and angle deformations of the polymer chains. Furthermore, the CNT junction demonstrated a more profitable reinforcement efficiency compared to conventional straight CNTs in the PE matrix. Compared to the ordinary CNT/PE model, the improvements in the Young’s modulus and toughness induced by the CNT junction were up to 60% and 25%. This is attributed to the reduced mobility induced by the geometry of the CNT junction and stronger interfacial interactions provided by the Stone–Wales defects of the CNT junction, slowing down the void propagation of the nanocomposite. With the understanding of the beneficial reinforcing effect of the CNT junction, this study provides valuable insights for the design and application of CNT-based networks in polymer nanocomposites.