Bitumen reinforced with carbon nanotubes (CNTs) exhibits excellent mechanical performance in pavement engineering. However, its nanoscale enhancement mechanisms have not yet been studied. This study utilizes molecular dynamics (MD) simulation to investigate the effects of CNTs on the load-induced cracking process in bitumen and elucidate fundamental insights into the interaction mechanism between the bitumen-CNT interface. The simulation results demonstrate that the aromatic rings in bitumen molecules can interact with the sp² carbon system of CNTs through π–π stacking, which enhances the load transfer efficiency and mechanical performance of bitumen. During the cracking process, the connected CNTs can bridge the nano-cracks, elongate the propagation path, and increase the overall fracture resistance. Moreover, the analysis of the energy contribution reveals that the pulling-out effect of CNTs can significantly increase their capacity to absorb external energy and save it as the non-bonded energy of the bitumen system, which results in a greater tolerance under external loading. However, debonding and sliding of the bitumen-CNT interface are observed during the cracking process, which weakens the interfacial bonding and reduces the strengthening effect. Future studies will be focused on improving the load-transfer efficiency at the interface to fully exploit the superior mechanical properties of CNTs.