Tribological properties of tread rubber is a key problem for the safety and durability of large aircraft tires. So, new molecular models of carbon nanotube (CNT) reinforced vulcanized natural rubber (VNR) composites have been developed to study the enhanced tribological properties and reveal the reinforced mechanism. Firstly, the dynamic process of the CNT agglomeration is discussed from the perspectives of fractional free volume (FFV) and binding energy. Then, a combined explanation of mechanical and interfacial properties is given to reveal the CNT-reinforced mechanism of the coefficient of friction (COF). Results indicate that the bulk, shear and Young’s modulus increase with the increasement of CNT, which are increasement of 19.13%, 21.11% and 26.89% in 15 wt.% CNT/VNR composite compared to VNR; the predicted results are consistent with the existing experimental conclusions, which can be used to reveal the CNT-reinforced mechanism of the rubber materials at atomic scale. It can also guide the design of rubber material prescription for aircraft tire. The molecular dynamics study provides a theoretical basis for the design and preparation of high wear resistance of tread rubber materials.