This study aims to investigate the influence of different spatial properties of asphalt molecular chains on the temperature self-healing behavior of asphalt nano-cracks. Molecular dynamics simulations and microscopic experiments were conducted to explore the microscopic mechanism of temperature self-healing in nano-cracks. Firstly, molecular structure models of virgin asphalt, aged asphalt, and tetra-tert-butylstyrene-based recycled asphalt were created, and their validity was verified. Secondly, by labeling the asphaltene components during the temperature self-healing process of the nano-cracks, the spatial characteristics of asphaltene molecular chains, such as the number of structural free volumes, the spatial angle of molecular chains, and the distribution characteristics of energy, were obtained. Finally, microscopic tests were conducted to examine the temperature self-healing behavior of different asphalt samples and the plausibility of the simulation. The results indicate that the temperature self-healing behavior of asphalt nano-cracks is influenced by the spatial configuration of the molecular chains, and different spatial structures have varying effects on the nano-cracks. The parallel distribution state greatly promotes the temperature self-healing of nano-cracks, followed by an angular stacking state. In contrast, side-to-side stacking impedes the temperature self-healing behavior of the nano-cracks. This study provides a microscopic perspective on the impact of different spatial properties of asphalt molecular chains on the temperature self-repair of asphalt nano-cracks, offering a theoretical foundation for the sustainable development of asphalt materials.